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]
Location

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]

Contents

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]

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 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

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. [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]

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). [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

GISAID Global initiative for sharing influenza virus data

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

CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) is a scientific research institute devoted primarily to biological research. It is a part of Council of Scientific and Industrial Research (CSIR), India.

National Centre for Disease Control Indian medical health government agency

The National Centre for Disease Control is an institute under the Indian Directorate General of Health Services, Ministry of Health and Family Welfare. It was established in July 1963 for research in epidemiology and control of communicable diseases and to reorganize the activities of the Malaria Institute of India. It has eight branches at Alwar, Bengaluru, Trivandrum, Calicut, Coonoor, Jagdalpur, Patna, Rajahmundry and Varanasi to advise the respective state governments on public health. The headquarters are in Sham Nath Marg, in New Delhi.

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.

COVID-19 vaccine Vaccine designed to provide acquired immunity against SARS-CoV-2

A COVID‑19 vaccine is a vaccine intended to provide acquired immunity against severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), the virus that causes coronavirus disease 2019 (COVID‑19). Prior to the COVID‑19 pandemic, an established body of knowledge existed about the structure and function of coronaviruses causing diseases like severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS). This knowledge accelerated the development of various vaccine platforms during early 2020. The initial focus of SARS-CoV-2 vaccines was on preventing symptomatic, often severe illness. On 10 January 2020, the SARS-CoV-2 genetic sequence data was shared through GISAID, and by 19 March, the global pharmaceutical industry announced a major commitment to address COVID-19. The COVID‑19 vaccines are widely credited for their role in reducing the spread, severity, and death caused by COVID-19.

SARS-CoV-2 Alpha variant Variant of SARS-CoV-2, the virus that causes COVID-19

The Alpha variant, also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several variants of concern, the variant is estimated to be 40–80% more transmissible than the wild-type SARS-CoV-2. It was first detected in November 2020 from a sample taken in September in the United Kingdom, and began to spread quickly by mid-December, around the same time as infections surged. This increase is thought to be at least partly because of one or more mutations in the virus' spike protein. The variant is also notable for having more mutations than normally seen.

SARS-CoV-2 Beta variant Variant of the SARS-CoV-2 virus

Beta variant, also known as lineage B.1.351, is a variant of SARS-CoV-2, the virus that causes COVID-19. One of several SARS-CoV-2 variants believed to be of particular importance, it was first detected in the Nelson Mandela Bay metropolitan area of the Eastern Cape province of South Africa in October 2020, which was reported by the country's health department on 18 December 2020. Phylogeographic analysis suggests this variant emerged in the Nelson Mandela Bay area in July or August 2020.

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

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has many variants; some are believed, or have been believed, to be of particular importance due to their potential for increased transmissibility, increased virulence, or reduced effectiveness of vaccines against them.

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.

Phylogenetic Assignment of Named Global Outbreak Lineages SARS-CoV-2 lineage nomenclature

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.

Centre for Genomic Pathogen Surveillance Computational genomics research institute in South Cambridgeshire

The Centre for Genomic Pathogen Surveillance is a computational genomics research institute in South Cambridgeshire.

Variant of concern Newly emerged variant of a virus with transmissibility and virulence that causes concerns

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Jemma Louise Geoghegan is a Scottish-born evolutionary virologist, based at the University of Otago, New Zealand, who specialises in researching emerging infectious diseases and the use of metagenomics to trace the evolution of viruses. As a leader in several government-funded research projects, Geoghegan became the public face of genomic sequencing during New Zealand's response to COVID-19. Her research has contributed to the discussion about the likely cause of coronavirus and the challenges around predicting pandemics. She was a recipient of the Young Tall Poppy Award in 2017 and the Rutherford Discovery Fellowship in 2020.

SARS-CoV-2 Delta variant Variant of SARS-CoV-2

The Delta variant is a variant of SARS-CoV-2, the virus that causes COVID-19. It was first detected in India in late 2020. The Delta variant was named on 31 May 2021 and had spread to over 163 countries by 24 August 2021. The World Health Organization (WHO) indicated that the Delta variant is becoming the dominant strain globally.

INSACOG is the forum set up under the Ministry of Health and Family Welfare by the Government of India on 25 December 2020, to study and monitor genome sequencing and virus variation of circulating strains of COVID-19 in India. Initially it was tasked to study the virus variant Lineage B.1.1.7 earlier found in United Kingdom in December 2020. INSACOG works as a consortium of 28 national laboratories for genome sequencing located in different parts of India. All these 10 laboratories are required to share 5% of positive samples to INSACOG for further research and studies. A National Centre for Disease Control (NCDC) nodal unit maintain a database of all samples of the new variants. Two national genomic sequencing database centers are appointed 1) National Institute of Biomedical Genomics and 2) CSIR Institute of Genomics and Integrative Biology. In its early research INSACOG identefied virus variant Lineage B.1.617 referred to as a double mutation variant.

Christian Happi is a Professor of Molecular Biology and Genomics in the Department of Biological Sciences and the Director of African Centre of Excellence for Genomics of Infectious Diseases, both at Redeemer’s University. He is known for leading the team of scientists that used genomic sequencing to identify a single point of infection from an animal reservoir to a human in the Ebola outbreak in West Africa. His research focus is on infectious diseases, including malaria, Lassa fever, Ebola virus disease, HIV and SARS-CoV-2.

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

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.

References

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