About the COVID-19 UK (COG-UK) Consortium

The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, represents a major threat to health in the UK and globally. To fully understand the transmission and evolution of the virus requires sequencing and analysing viral genomes at scale and speed. The numbers of samples calls for a rapid increase in the UK’s pathogen genome sequencing capacity rapidly and robustly.

To provide this increased capacity to collect, sequence and analyse the whole genomes of virus samples in the UK, the COVID-19 Genomics UK (COG-UK) consortium is pooling the world leading knowledge and expertise in genomics of the four UK Public Health Agencies, multiple regional University hubs, and large sequencing centres such as the Wellcome Sanger Institute. Below is a listing of all the funders, academic organisations, NHS organisations and collaborators working together within COG-UK who have come together to meet this need.

If you would like to know more about COVID-19 – the latest understanding and facts about how the virus works, how it is spread and how to control it – please visit the UKRI website: Coronavirus: the science explained.

Funders

The following organisations have contributed a combined £20 million to support the work of the Consortium:

Department of Health and Social Care

Find out more about the Department of Health and Social Care at:

https://www.gov.uk/government/organisations/department-of-health-and-social-care

UK Research and Innovation (UKRI)

UKRI works in partnership with universities, research organisations, businesses, charities, and government to create the best possible environment for research and innovation to flourish. We aim to maximise the contribution of each of our component parts, working individually and collectively. We work with our many partners to benefit everyone through knowledge, talent and ideas. Operating across the whole of the UK with a combined budget of more than £7 billion, UK Research and Innovation brings together the seven research councils, Innovate UK and Research England.

https://www.ukri.org/

Wellcome

Wellcome exists to improve health by helping great ideas to thrive. We support researchers, we take on big health challenges, we campaign for better science, and we help everyone get involved with science and health research. We are a politically and financially independent foundation.

https://wellcome.ac.uk/

 

Partners

The following academic universities, institutions, Public Health groups and NHS organisations are working together in the Consortium:

Belfast Health and Social Care Trust

Contributors:

The Belfast Health and Social Care Trust (BHSCT) Regional Virus Laboratory team are working in partnership with Queen’s University Belfast and BHSCT Regional Genetics Laboratory to sequence SARS-CoV-2 samples from patients in Northern Ireland as part of the COG-UK consortium.

http://www.belfasttrust.hscni.net/

Cardiff University

Contributors:

The Cardiff team are supporting the project through the use of the MRC CLIMB node hosted at Cardiff, which will provide computational capacity for analysis and data storage for the consortium. The bioinformatics and sequencing staff in the School of Biosciences are also working as part of the PHW Pathogen Genomics effort to manage, sequence and analyse SARS-COV-2 samples collected in Wales.

https://www.cardiff.ac.uk/

EMBL-EBI (European Bioinformatics Institute)

Contributor:

  • Dr Guy Cochrane, Team Leader, Data Coordination and Archiving and Head of the European Nucleotide Archive (ENA)
  • Dr Zamin Iqbal, Research Group Leader

https://www.ebi.ac.uk/

Genomics England Limited

Genomics Partnership Wales

Genomics Partnership Wales (GPW) is the entity setup by Welsh Government to deliver the Welsh Genomics for Precision Medicine Strategy. GPW is the umbrella for pathogen and human genomics work in the NHS in Wales, and is supporting the Pathogen Genomics work being undertaken in Wales.

Contributor:

https://genomicspartnership.wales/

Imperial College London

Contributors:

https://www.imperial.ac.uk/

MRC-University of Glasgow Centre for Virus Research

The mission of the MRC-Centre for Virus research is to carry out fundamental research on viruses and viral diseases, translating the knowledge gained for the improvement of health and the benefit of society.

Contributors:

https://www.gla.ac.uk/researchinstitutes/iii/cvr/

Public Health Agency

Contributors:

https://www.publichealth.hscni.net/

Public Health England

Public Health England aims to address urgent threats to health in the 21st century. The organisation has been central to the national response to COVID-19, and has led this proposal to develop a national capability to sequence the causative virus and use this to inform public health interventions.

The COVID-19 Genomics UK (COG-UK) Consortium will be led by Sharon Peacock as a collaborative initiative to capture information on the virus and from patients so as to reduce the impact from the COVID-19 epidemic in the UK.

Contributors:

https://www.gov.uk/government/organisations/public-health-england

Public Health Scotland

Contributors:

https://www.hps.scot.nhs.uk/

Public Health Wales NHS Trust

Public Health Wales NHS Trust (PHW) is the national public health authority for Wales. PHW works to protect and improve health and well-being and reduce health inequalities for the people of Wales. PHW is leading the national response to COVID-19 in Wales. PHW operates diagnostic laboratories across Wales and has been providing SARS-COV-2 testing in Wales. In addition, PHW epidemiology teams have been providing support across Wales to track cases and support management of the outbreak. Sequencing of Welsh samples is being undertaken by the Pathogen Genomics Unit (PenGU). PenGU was formally launched in 2018, and provides an accredited sequencing environment for a range of clinical pathogen genomics services for the whole of Wales.

Contributors:

The Pathogen Genomics team in Public Health Wales will be contributing to COG-UK by sequencing and analysing Welsh SARS-COV-2 cases. Data that is being generated is being fed back in real time to clinical colleagues across the NHS in Wales as well as feeding into outbreak management and planning within the Welsh NHS and Welsh Government. In addition to sequencing samples, the team are providing bioinformatics support to build production-ready pipelines for processing samples, supporting the development of systems on CLIMB for consortium use and leading efforts to enable metadata sharing across the UK.

https://phw.nhs.wales/

Quadram Institute

Contributors:

https://quadram.ac.uk/

Queen's University Belfast

The Centre for Genomic Pathogen Surveillance

Contributors:

https://www.pathogensurveillance.net/

University College London

Contributors:

Leading the sequencing initiative at UCL are:

The team have been working in joint partnership with Virology at Imperial College Healthcare NHS Trust; Dr David Muir and Dr Paul Rendell to deliver the pipeline of sequencing data.

 

Pathogen Genomics Unit
Pathogen Genomics Unit
UCL Genomics
UCL Genomics

UCL and Imperial are also leading the COG-UK Hospital-Onset COVID-19 Infections (HOCI) Study; A phase III prospective, interventional, cohort, superiority study to evaluate the benefit of rapid COVID-19 genomic sequencing (the COVID-19 GENOMICS UK project) on infection control in preventing the spread of the virus in United Kingdom NHS hospitals. COG-UK collaborators include Glasgow, Sheffield and Guys and St Thomas’ Trust

 

https://www.ucl.ac.uk/

University of Birmingham

Contributors:

The team will be drawing on ARTIC and CLIMB. The CLIMB project, which recently secured funding for a further five years with the CLIMB-BIG-DATA project, will provide the data analysis pipelines, computing and storage capacity required.

The ARTIC project, funded by a Wellcome Trust Collaborative Award, is a collaborative project to put genomics at the heart of outbreak response

https://www.birmingham.ac.uk/index.aspx

University of Cambridge

Contributors:

https://www.cam.ac.uk/

University of Edinburgh

Contributors:

https://www.ed.ac.uk/

University of Exeter

Contributors:

  • Dr Stephen Michell, Senior Lecturer in Molecular Microbiology, College of Life and Environmental Sciences
  • Dr Ben Temperton, Senior Lecturer in Bioinformatics, College of Life and Environmental Sciences
  • Dr Aaron Jeffries, Senior Research Fellow, University of Exeter Medical School
  • Professor David Studholme, Associate Professor in Bioinformatics, College of Life and Environmental Sciences
  • Dr Jane Masoli, Academic Geriatrician, Royal Devon and Exeter NHS Trust and University of Exeter Medical School

The team is working closely with the Clinical Diagnostics teams at the Royal Devon and Exeter NHS Trust and in the surrounding area.

https://www.exeter.ac.uk/

University of Liverpool

Contributors:

https://www.liverpool.ac.uk/

University of Northumbria

Contributor:

  • Dr Darren Smith, Associate Professor in Bacteriophage Biology, Department of Applied Biology, Cellular and Molecular Sciences/Microbiology Group, University of Northumbria

Dr Smith is the academic lead for the DNA sequencing research facility at Northumbria University, NU-OMICS that is linked to both academic and industrially linked DNA sequencing projects

https://www.northumbria.ac.uk/

University of Nottingham

Contributors:

  • Professor Matt Loose, Academic Lead for DeepSeq, Developmental and Computational Biology, School of Life Sciences, Faculty of Medicine & Health Sciences
  • Professor Jonathan Ball, Professor of Molecular Virology, School of Life Sciences, Faculty of Medicine & Health Sciences

The team is working closely with the Clinical Pathology team at Nottingham University Hospitals. The University of Nottingham next generation sequencing platform, DeepSeq, is providing sequencing expertise and the Virology groups are helping support access to samples.

https://www.nottingham.ac.uk/

University of Oxford

Contributors:

http://www.ox.ac.uk/

University of Portsmouth

Contributor:

  • Dr Samuel Robson, Senior Research Fellow and Bioinformatics Lead at the University of Portsmouth and the Centre for Enzyme Innovation (CEI).
  • Dr Yann Bourgeois, Lecturer in School of Biological Sciences
  • Angela Beckett, Specialist Research Technician, Centre for Enzyme Innovation

The University of Portsmouth Team are currently working in partnership with Portsmouth Hospitals NHS Trust:

  • Professor Anoop Chauhan, Respiratory Physician, Portsmouth Hospitals NHS Trust
  • Dr Sharon Glaysher, Specialist Biomedical Scientist and Translational Research Laboratory Manager, Portsmouth Hospitals NHS Trust
  • Scott Elliott, Specialist Biomedical Scientist and and Translational Research Laboratory Manager, Portsmouth Hospitals NHS Trust
  • Ethan Butcher, Research Associate Practitioner, Portsmouth Hospitals NHS Trust
  • Kelly Bicknell, Clinical Scientist (Virology), Portsmouth Hospitals NHS Trust
  • Dr Sarah Wyllie, Consultant Microbiologist and infection control lead, Portsmouth Hospitals NHS Trust
  • Allyson Lloyd, Microbiology Laboratory Manager, Portsmouth Hospitals NHS Trust

https://www.port.ac.uk/

University of Sheffield

Contributors:

  • Dr Thushan de Silva, Senior Clinical Lecturer and Honorary Consultant Physician in Infectious Diseases, University of Sheffield Department of Infection, Immunity and Cardiovascular Disease
  • Dr Matthew Parker, Sheffield Bioinformatics Core at the National Institute of Health Research (NIHR) Sheffield Biomedical Research Centre
  • Members of the research team: Adri Angyal, Rebecca Brown, Matthew Wyles, Luke Green, Rachel Tucker, Paul Parsons, Danielle Groves, Laura Carrilero, Katie Johnson, Nikki Smith and others: https://www.sheffield.ac.uk/medicine/research/research-themes/infection/covid-19

The team is working in partnership with Consultant Virologists Dr Cariad Evans, Dr Mohammad Raza and Dr Alison Cope, Academic Clinical Fellows Dr Alex Keeley and Dr Benjamin Lindsey, and Consultant Microbiologist Dr Dave Partridge at the Sheffield Teaching Hospitals NHS Foundation Trust’s regional NHS virology laboratory based at the Northern General Hospital.

https://www.sheffield.ac.uk/

Wellcome Sanger Institute

Contributors:

The Wellcome Sanger Institute has a large team working to support the COG-UK network led by Dr Cordelia Langford, Ian Johnston, Dr Alex Alderton, Dr Matt Berriman, Dr Mara Lawniczak, Professor David Aanensen, John Sillitoe and Professor Dominic Kwiatkowski. Dr Ewan Harrison serves as Project Manager responsible for overall coordination of the COG-UK network.

The full of contributors can be seen here: https://www.sanger.ac.uk/covid-team

https://www.sanger.ac.uk/

West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde