COVID-19 Genomics UK Consortium

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COVID-19 Genomics UK
New COG-UK logo.jpg
EstablishedApril 2020
Focus COVID-19 genomic sequencing
Key people Sharon Peacock
Budget£20 million [1]

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]


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]


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 theCOVID-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


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 people

The executive director of the consortium is Sharon Peacock, a professor and microbiologist at Cambridge University. [23] [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. [24]


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

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. [23] 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'. [28]

Selected publications

Related Research Articles

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GISAID 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 pandemic. On January 10, 2020, the first whole-genome sequences of SARS-CoV-2 were made available on GISAID, which enabled global responses to the pandemic, including the development of the first vaccines and diagnostic tests to detect SARS-CoV-2. GISAID facilitates genomic epidemiology and real-time surveillance to monitor the emergence of new COVID-19 viral strains across the planet.

Institute of Genomics and Integrative Biology

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National Centre for Disease Control Indian medical health government agency

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Dr. Vinod Scaria FRSB is an Indian biologist, medical researcher pioneering in Precision Medicine and Clinical Genomics in India. He is best known for sequencing the first Indian genome. He was also instrumental in the sequencing of The first Sri Lankan Genome, analysis of the first Malaysian Genome sequencing and analysis of the Wild-type strain of Zebrafish and the IndiGen programme on Genomics for Public Health in India

The 100,000 Genomes Project is a now-completed UK Government project managed by Genomics England that is sequencing whole genomes from National Health Service patients. The project is focusing on rare diseases, some common types of cancer, and infectious diseases. Participants give consent for their genome data to be linked to information about their medical condition and health records. The medical and genomic data is shared with researchers to improve knowledge of the causes, treatment and care of diseases.

Sharon Peacock is a British microbiologist who is Professor of Public Health and Microbiology in the Department of Medicine at the University of Cambridge. She is known for her work on the use of microbial whole genome sequencing in diagnostic and public health microbiology, particularly on the bacterium Burkholderia pseudomallei and on methicillin-resistant Staphylococcus aureus (MRSA).

Severe acute respiratory syndrome coronavirus 2 Virus that causes COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), also known as the coronavirus, is the virus that causes COVID-19, the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus was previously referred to by its provisional name, 2019 novel coronavirus (2019-nCoV), and has also been called human coronavirus 2019. First identified in the city of Wuhan, Hubei, China, the World Health Organization declared the outbreak a Public Health Emergency of International Concern on 30 January 2020, and a pandemic on 11 March 2020. SARS‑CoV‑2 is a positive-sense single-stranded RNA virus that is contagious in humans. As described by the US National Institutes of Health, it is the successor to SARS-CoV-1, the virus that caused the 2002–2004 SARS outbreak.

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Variants of SARS-CoV-2 Notable variants of SARS-CoV-2

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SARS-CoV-2 Gamma variant Variant of the SARS-Cov-2 virus

Gamma variant, also known as lineage P.1, is one of the variants of SARS-CoV-2, the virus that causes COVID-19. This variant of SARS-CoV-2 has been named lineage P.1 and has 17 amino acid substitutions, ten of which are in its spike protein, including these three designated to be of particular concern: N501Y, E484K and K417T. This variant of SARS-CoV-2 was first detected by the National Institute of Infectious Diseases (NIID) of Japan, on 6 January 2021 in four people who had arrived in Tokyo having visited Amazonas, Brazil, four days earlier. It was subsequently declared to be in circulation in Brazil. Under the simplified naming scheme proposed by the World Health Organization, P.1 has been labeled Gamma variant, and is currently considered a variant of concern.

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The Phylogenetic Assignment of Named Global Outbreak Lineages (PANGOLIN) is a software tool developed by members of the laboratory of Andrew Rambaut, with an associated web application developed by the Centre for Genomic Pathogen Surveillance in South Cambridgeshire. Its purpose is to implement a dynamic nomenclature to classify genetic lineages for SARS-CoV-2, the virus that causes COVID-19. A user with a full genome sequence of a sample of SARS-CoV-2 can use the tool to submit that sequence, which is then compared with other genome sequences, and assigned the most likely lineage. Single or multiple runs are possible, and the tool can return further information regarding the known history of the assigned lineage. Additionally, it interfaces with Microreact, to show a time sequence of the location of reports of sequenced samples of the same lineage. This latter feature draws on publicly available genomes obtained from the COVID-19 Genomics UK Consortium and from those submitted to GISAID. It is named after the pangolin.

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Zeta variant, also known as lineage P.2, is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in the state of Rio de Janeiro; it harbors the E484K mutation, but not the N501Y and K417T mutations. It evolved independently in Rio de Janeiro without being directly related to the Gamma variant from Manaus.


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