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COVID-19 Genomics UK Consortium

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COVID-19 Genomics UK
EstablishedApril 2020
FocusCOVID-19 genomic sequencing
Key peopleSharon Peacock
Budget£32.2 million[1]
Location
United Kingdom

The COVID-19 Genomics UK (COG-UK) consortium was a group of academic institutions and public health agencies in the United Kingdom created in April 2020[1][2][3] to collect, sequence and analyse genomes of SARS-CoV-2 at scale, as part of COVID-19 pandemic response.

The genome data generated by COG-UK was integrated with epidemiological data and patient health records to monitor introductions into the UK, community transmission and outbreaks of SARS-CoV-2; to assess changes in transmissibility and virulence; and to evaluate the impact of treatments and non-pharmaceutical interventions. COG-UK members also undertook research that integrated human genomic and health data to understand the biology of SARS-CoV-2 and its impact on those infected.[4]

The consortium identified the SARS-CoV-2 Alpha variant (at the time, referred to as Variant of Concern 202012/01) in November 2020, which became the subject of subsequent investigations by the UK public health agencies, coordinated by Public Health England and supported by COG-UK.[5][6]

Between April and September 2021, SARS-CoV-2 sequencing transitioned to become a public health-led national service[7] after which COG-UK focused on data linkage, research and international training.[8]

The consortium formally closed at the end of March 2023.[9]

Funding

COG-UK was supported by £20 million funding from the Department of Health and Social Care, UK Research and Innovation (UKRI), and the Wellcome Sanger Institute.[1]

The consortium received a further £12.2 million from the Department of Health and Social Care's Testing Innovation Fund in November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the 2020-2021 winter period.[10]

Together with Wellcome Connecting Science (WCS), COG-UK was also awarded a Foreign, Commonwealth & Development Office/Wellcome Epidemic Preparedness Coronavirus grant of nearly £1 million to develop COG-Train, a learning programme to support the global scientific and public health community in SARS-CoV-2 genome sequencing.[11]

Structure[edit]

The consortium comprised the four UK public health agencies, the Wellcome Sanger Institute, sixteen academic partners, and National Health Service organisations. It adopted a Hub and Spoke model with a centralised administrative hub (University of Cambridge), a national sequencing hub (Sanger Institute), and sequencing and analysis capacity regionally distributed across all partners.[12]

Samples from COVID-19 patients were collected by NHS laboratories, public health laboratories and national coronavirus testing centres and sent to partner sites for sequencing. Viral genome sequencing was undertaken by the four UK public health agencies, the Wellcome Sanger Institute, the Quadram Institute, and fifteen 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.[13]

The rapid launch and delivery of SARS-CoV-2 genome sequencing data was enabled by use of the pre-existing infrastructure and expertise of COG-UK partners and members. For example, COG-UK relied on the Cloud Infrastructure for Microbial Bioinformatics (CLIMB),[14] which was launched in 2014 with support from the Medical Research Council. CLIMB is an open, cloud-based computing infrastructure for developing and sharing datasets and bioinformatics software, tools and methods to interpret ‘big data’.[15] CLIMB is a partnership between the Universities of Bath, Birmingham, Cardiff, Leicester, Swansea and Warwick, the London School of Hygiene and Tropical Medicine and the Quadram Institute.[16]

Genome data for each positive sample sequenced was linked to the person who provided the sample using an anonymous code. These were uploaded to CLIMB-COVID where the genomes could be characterised, which included assigning each genome to a lineage and detecting mutations. Public health agencies were then able to access this information and link it to detailed public health information.[17]

Key people[edit]

The executive director and chair of the consortium was Sharon Peacock, a professor and microbiologist at the University of Cambridge.[18][19]

More than 600 consortium members contributed to the work of COG-UK between April 2020 and the end of March 2023[1], with key roles fulfilled by researchers from across the consortium partners [2], and a management team based at the University of Cambridge [3].

Impact[edit]

COG-UK pioneered early and large-scale coordinated national sequencing of SARS-CoV-2 viral genomes, along with the open and rapid sharing of genomic data.

By December 2020, COG-UK had sequenced the genomes of more than 150,000 samples of SARS-CoV-2 virus and uploaded them to GISAID, representing around 5% of all UK COVID-19 cases. Approximately 60% of these were sequenced at the Wellcome Sanger Institute. By December 2021, the UK had sequenced over 1.8 million SARS-CoV-2 genomes.

The insights arising from analysis of these genome data had a range of impacts during the COVID-19 pandemic response:[20]

  1. Enabling the identification and monitoring of "Variants of Concern" and "Variants under Investigation" to inform public health actions and policy decisions.[19]
  2. Tracking the introduction and spread of COVID-19 to inform border control, outbreak management and public health policies.[21]
  3. Facilitating key UK COVID-19 studies:
    • The COG-UK HOCI (Hospital-Onset COVID-19 Infections) study[22][23][24]
    • The Office of National Statistics (ONS) COVID-19 Infection Survey (CIS) [25][26]
    • The Real-time Assessment of Community Transmission (REACT) Study [27][28]
    • The Vivaldi study [29][30]
    • The Oxford Vaccine trial [31]
    • The Novavax Vaccine trial [32]
  4. Furthering understanding of the biology and evolution of the SARS-CoV-2 virus to guide treatments, vaccine development and diagnostics.[33]
  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.[34]

By September 2021, COG-UK pivoted to focus on three strategic areas:[8]

  1. Enhancing the value of viral genome sequence data through more extensive data linkage, including human genome data and clinical datasets.
  2. Advancing research on SARS-CoV-2 transmission, variants, methods and analysis tools.
  3. Coordinating a global SARS-CoV-2 genomics training programme (COG-Train).

Data linkage & Analysis

By linking and analysing different types of data, it is possible to undertake more in depth research and generate new understanding about the differences in the transmission of SARS-CoV-2 variants and the disease that they cause.

COG-UK collaborated with partners through the UK Health Data Research Alliance and the Outbreak Data Analysis Platform (ODAP) to link viral genome data with other complex datasets.[35][36]

Through these collaborations, SARS-CoV-2 sequencing data has been linked to a number of different datasets including:

  • Host sequencing (GenOMICC and UK research cohorts)
  • Clinical severity (ISARIC 4C, ICNARC CMP)
  • Hospitalisation outcomes (PHOSP-COVID)
  • Acute care admissions data (England and Wales)
  • Vaccination data
  • Infection control in hospitals (HOCI data)

All such linked data are stored securely with controlled access through approved pathways to maintain patient privacy and ensure appropriate usage and attribution.[37]

Research

COG-UK provided seed funding for consortium members to undertake research projects that would generate novel insights relevant to the COVID-19 pandemic, and to prepare for future pandemics.[38]

These projects focussed on:

  1. Monitoring and understanding the emergence of SARS-CoV-2 variants with the potential to transmit more readily and/or circumvent immunity.
  2. Integrating pathogen genome data with diagnostic and rapid genotyping data to strengthen pandemic preparedness.
  3. Developing online resources to improve access to quality control processes for SARS-CoV-2 genome data.
  4. Improving linkage and integration of genomic data with different types of epidemiological and clinical metadata.
  5. Developing metagenomic technologies for the surveillance of known and unknown pathogens with the potential to impact human health.

COG-UK also provided seed funding for consortium members to support early career scientists reinvigorate research projects delayed owing to time spent on the pandemic response.[39]

Training

Together with Wellcome Connecting Science, COG-UK established a free international online learning programme in using genomics to investigate SARS-CoV-2 and other infectious diseases.

Known as COG-Train, the programme sought to ‘facilitate an increase global genome sequencing and analysis capacity, reduce sequencing inequality and enhance pathogen surveillance’. Its training courses were built through partnerships with international researchers, public health experts and surveillance networks.

Outputs of COG-Train included a series of massive online, open-access courses on all aspects of SARS-CoV-2 sequencing, as well as week-long intensive virtual training courses, short expert workshops and concurrent distributed classrooms.[40]

Funded by the Wellcome Trust and the Foreign, Commonwealth & Development Office, COG-Train delivered free online training to thousands of learners in more than 100 countries worldwide. Its three week course ‘The Power of Genomics to Understand the COVID-19 Pandemic’ remains available through the FutureLearn platform.

Protocol and tool development[edit]

Protocols and tools developed by COG-UK consortium members were used globally during the first three years of the COVID-19 pandemic and continue to be of utility today. These include:

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.[19] Approximately 60% of these were sequenced at the Wellcome Sanger Institute[18] and the COG-UK consortium was reported to have understood 'the genetic history of more than 150,000 samples of SARS-CoV-2 virus'.[49]

According to the COG-UK website, by December 2021, the UK had sequenced over 1.8 million SARS-CoV-2 genomes.[50]

Events

Seminars and showcases

COG-UK ran a series of events to share the advances and discoveries arising from the work of consortium members and to provide forums for discussion. These included seminars and science showcases,[51][52] where consortium members have shared their analyses and insights with each other and the public.

In October 2021, the COG-UK Together event saw members from across the consortium join a mixed online/in person event to share their experiences during the first 18 months of the pandemic.[53]

Women in COG

Consortium members also organised and hosted the ‘Women in COG’ interview series, which showcased the lives and work of inspirational women (and male supporters/allies) from the COG-UK network and outside of the consortium. Interviewees included:

  • Dr Charlotte Summers[54]

This series was also distilled into a book titled ‘Snapshots of Women in COG: Scientific Excellence during the COVID-19 pandemic’.

Legacy

Publications

COG-UK members produced more than 100 publications using the data, analysis and tools developed between April 2020 and March 2023.[67]

Rand Europe evaluation

An independent evaluation undertaken by Rand Europe reported that COG-UK made ‘diverse contributions to understanding and responding to the COVID-19 pandemic’ and ‘a significant and valuable contribution to the UK's public health genomics landscape’.[68]

The report identified the key COG-UK achievements as:

  1. Helping to advance scientific knowledge about SARS-CoV-2 and improve genome sequencing and analysis methodologies.
  2. Informing key policy and public health decisions made in response to the COVID-19 pandemic in the UK.
  3. Informing medical innovation efforts, including evaluation of vaccine efficacy against SARS-CoV-2 variants and their susceptibility to therapeutics.
  4. Influencing how decision makers value pathogen genomics in building effective public health systems.
  5. Strengthening the UK pathogen genomics capacity and ability to respond to future infectious disease threats.
  6. Influenced international SARS-CoV-2 sequencing initiatives.

History of COG-UK

The story of the consortium has been captured in ‘Cracking Covid: The history of COG-UK’, an exhibition curated by historian of medicine Dr Lara Marks which documents the work and achievements of COG-UK based on interviews with more than eighty consortium members. The exhibition is free to access through the ‘What is biotechnology’ platform.[69]

Selected publications[edit]

References[edit]

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  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."
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  21. ^ 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.
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  24. ^ Panca, M.; Blackstone, J.; Stirrup, O.; Cutino-Moguel, M.-T.; Thomson, E.; Peters, C.; Snell, L.B.; Nebbia, G.; Holmes, A.; Chawla, A.; Machin, N.; Taha, Y.; Mahungu, T.; Saluja, T.; de Silva, T.I. (September 2023). "Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals". Journal of Hospital Infection. 139: 23–32. doi:10.1016/j.jhin.2023.06.005. PMC 10257337. PMID 37308063.
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  27. ^ "Real-time Assessment of Community Transmission (REACT) Study". Archived from the original on 6 July 2020.
  28. ^ Eales, Oliver; Haw, David; Wang, Haowei; Atchison, Christina; Ashby, Deborah; Cooke, Graham S.; Barclay, Wendy; Ward, Helen; Darzi, Ara; Donnelly, Christl A.; Chadeau-Hyam, Marc; Elliott, Paul; Riley, Steven (25 May 2023). Dushoff, Jonathan (ed.). "Dynamics of SARS-CoV-2 infection hospitalisation and infection fatality ratios over 23 months in England". PLOS Biology. 21 (5): e3002118. doi:10.1371/journal.pbio.3002118. ISSN 1545-7885. PMC 10212114. PMID 37228015.
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  31. ^ 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.
  32. ^ "PREVENT-19: A COVID-19 vaccine candidate clinical trial". Archived from the original on 28 December 2020.
  33. ^ 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 (1): 161–172. doi:10.1002/jmv.27285. ISSN 1096-9071. PMC 8426849. PMID 34415583.
  34. ^ 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.
  35. ^ "Why COG-UK is joining the UK Health Data Research Alliance". HDR UK. Retrieved 23 January 2024.
  36. ^ "Outbreak Data Analysis Platform". ODAP - Outbreak Data Analysis Platform. Retrieved 23 January 2024.
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  38. ^ "WhatisBiotechnology • The sciences, places and people that have created biotechnology". WhatisBiotechnology.org. Retrieved 23 January 2024.
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  45. ^ O'Toole, Áine; Hill, Verity; Pybus, Oliver G.; Watts, Alexander; Bogoch, Issac I.; Khan, Kamran; Messina, Jane P.; The COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; Tegally, Houriiyah; Lessells, Richard R.; Giandhari, Jennifer; Pillay, Sureshnee; Tumedi, Kefentse Arnold (17 September 2021). "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch". Wellcome Open Research. 6: 121. doi:10.12688/wellcomeopenres.16661.2. ISSN 2398-502X. PMC 8176267. PMID 34095513.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  46. ^ "Cov-Lineages". cov-lineages.org. Retrieved 23 January 2024.
  47. ^ "COG-UK/Mutation Explorer". sars2.cvr.gla.ac.uk. Retrieved 23 January 2024.
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  52. ^ COG-UK Science Showcase March 2021, retrieved 23 January 2024
  53. ^ "COG-UK Together - YouTube". www.youtube.com. Retrieved 23 January 2024.
  54. ^ COG-UK's first 'Women in COG' event, featuring Dr Charlotte Summers, retrieved 23 January 2024
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  56. ^ COG-UK's 'Women in COG' event with Angela Douglas MBE, retrieved 23 January 2024
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  68. ^ Marjanovic, Sonja; Romanelli, Robert J.; Ali, Gemma-Claire; Leach, Brandi; Bonsu, Margaretha; Rodriguez-Rincon, Daniela; Ling, Tom (31 August 2022). "COVID-19 Genomics UK (COG-UK) Consortium: Final Report". Rand Health Quarterly. 9 (4): 24. ISSN 2162-8254. PMC 9519096. PMID 36238008.
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External links[edit]

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