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

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

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 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/

The Wellcome Sanger Institute, is supplying supplying financial, technical, research and administrative support to the work of the COVID-19 Genomics UK Consortium (COG-UK)

https://www.sanger.ac.uk

Contributors:

• Dr Derek Fairley, (Regional Virus Laboratory)
• Dr Tanya Curran, (Regional Virus Laboratory)
• Dr James McKenna, (Regional Virus Laboratory)
• Molecular Typing team (Regional Virus Laboratory)

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/

Contributors:

• Dr Tom Connor, Reader, School of Biosciences, Cardiff University and Consultant Bioinformatician/Pathogen Bioinformatics Lead, Public Health Wales NHS Trust
• Dr Anna Price, Research Software Engineer (Supercomputing Wales and CLIMB-BIG-DATA)
• Joel Southgate,  Research Student, School of Biosciences
• Advanced Research Computing at Cardiff / Supercomputing Wales

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/

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/

Contributor:

• Professor Sir Mark Caulfield, Chief Scientist

https://www.genomicsengland.co.uk/

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:

• Michaela John, Programme manager

https://genomicspartnership.wales/

Contributors:

• Professor Neil Ferguson, Faculty of Medicine, School of Public Health
• Dr Erik Volz, Faculty of Medicine, School of Public Health

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

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:

• Professor Emma Thomson, MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation
• Professor David Robertson, Head of Viral Genomics and Bioinformatics
• Dr Ana Da Silva Filipe, Head of Genomics
• James Shepherd, CVR clinical fellow
• Dr Kathy Li, CVR clinical fellow
• Natasha Jesudason, CVR clinical fellow
• Rajiv Shah, CVR clinical fellow
• Dr Kathy Smollett, CVR research associate – genomics
• Dr Stephen Carmichael, CVR research associate – genomics
• Dr Lilly Tong, CVR research associate – genomics
• Natasha Johnson, CVR technician – genomics
• Daniel Mair, CVR technician – genomics
• Jenna Nichols, CVR technician – genomics
• Dr Richard Orton, CVR bioinformatician
• Dr Joseph Hughes, CVR bioinformatician
• Dr Sreenu Vattipally, CVR bioinformatician
• Dr Josh Singer, CVR software engineer
• Dr Elihu Aranday-Cortes,  CVR Research Associate
• Dr Kyriaki Nomikou, CVR Senior Research Fellow
• Dr Yasmin A Parr, CVR Research Assistant
• Dr Kirstyn Brunker, Research Associate, Institute of Biodiversity, Animal Health & Comparative Medicine
• Ms Alice Broos, CVR Research Technician

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

Contributors:

• Dr Kate Templeton, Consultant Clinical Scientist, Royal Infirmary Edinburgh
• Martin McHugh, Clinical Scientist, Royal Infirmary Edinburgh
• Dr Rebecca Dewar, Clinical Scientist, Royal Infirmary Edinburgh

https://www.nhslothian.scot/

Contributors:

• Dr Tim Wyatt, Consultant Microbiologist
• Dr Declan Bradley, Consultant in Public Health Medicine and Clinical Lecturer in Public Health

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

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:

• Professor Sharon Peacock, Director of the COVID-19 Genomics UK (COG-UK) Consortium and Director of the National Infection Service, Public Health England
• Richard Myers, Interim Head of Bioinformatics, PHE Core Bioinformatics Unit
• Professor Saheer Gharbia, Genomics Research Unit
• Dr Tamyo Mbisa, Head of the Antiviral Unit and Clinical Scientist at the Virus Reference Department at Public Health England
• Dr Angie Lackenby, Sequencing Lead, Clinical Scientist, Respiratory Virus Unit, Virus Reference Department, National Infection Service
• Dr Shahjahan Miah, Technical Lead for Sequencing, Respiratory Virus Unit, Virus Reference Department, National Infection Service
• Dr Steven Platt, Bioinformatician, Respiratory Virus Unit, Virus Reference Department, National Infection Service
• Dr Jonathan Hubb, Head of Central Sequencing Laboratory, National Infection Service
• Dr Meera Chand, consultant microbiologist
• Dr Gavin Dabrera, Consultant Epidemiologist
• Dr Mary Ramsay, Head of Immunisations
• Dr Daniel Bradshaw, Consultant Virologist

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

Contributors:

• Professor Matthew Holden, Public Health Scotland and University of St Andrews
• Dr Sharif Shaaban, Bioinformatician, Public Health Microbiology Team, Public Health Scotland
• Dr Alison Smith-Palmer, Senior Epidemiologist, Public Health Scotland
• Dr Michael Lockhart, Consultant Medical Microbiologist and Clinical Lead for the Public Health Microbiology team, Public Health Scotland

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

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:

• Dr Sally Corden, Pathogen Genomics Unit lead
• Dr Thomas Connor, Consultant Bioinformatician/Bioinformatics lead for Pathogen Genomics
• Dr Catherine Moore, Consultant Clinical Scientist, Wales Specialist Virology Centre
• Dr Simon Cottrell, Principle Epidemiologist, Communicable and Vaccine Preventable Diseases
• Joanne Watkins, Laboratory Senior, Pathogen Genomics Unit
• Dr Matt Bull, Senior Bioinformaticain, PHW Pathogen Bioinformatics
• Dr Sara Rey, Bioinformatician, PHW Pathogen Bioinformatics
• PHW Pathogen Genomics laboratory and Bioinformatics teams

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/

Contributors:

• Dr Justin O’Grady, Group Leader, Rapid infectious disease and foodborne pathogen diagnosis/detection
• Dr Andrew Page, Head of Informatics

https://quadram.ac.uk/

Contributor:

• Dr David Simpson, Senior Lecturer/Genomics Core Technology Unit

https://www.qub.ac.uk

Contributors:

• Professor David Aanensen, Director of the Centre for Genomic Pathogen Surveillance
• Dr Khalil Abudahab, Principal Software Developer
• Mirko Menegazzo, EpiCollect Lead
• Ben Taylor, Principal Software Developer
• Dr Anthony Underwood, Bioinformatics Implementation Manager
• Dr Corin Yeats, Computational Biologist

https://www.pathogensurveillance.net/

The UK Biocentre is hosting and managing the Milton Keynes Lighthouse Lab set up to provide diagnostic services for COVID-19 testing.

UK Biocentre is a subsidiary of UK Biobank and was established to share expertise of high-throughput sample handling with other academic partners. UK Biobank is a national health resource following the lives of 500,000 participants and providing key data for a wide range of health studies, including those into the COVID-19 pandemic.

Contributor:

• Dr Tony Cox, Chief Executive

https://www.ukbiocentre.com/

The Alderley Park, Cheshire Lighthouse Lab is supplying diagnostic services to the UK’s COVID-19 testing. The Lab is located in new dedicated labs at Bruntwood SciTech’s Alderley Park and is led by Medicines Discovery Catapult.

https://www.lighthouselabs.org.uk/

The Cambridge Lighthouse Lab has been set up to supply diagnostic services to the UK’s COVID-19 testing. AstraZeneca, GSK, and the University of Cambridge have formed a joint collaboration to setup the Cambridge Lighthouse Lab at the University’s Anne McLaren laboratory.

https://www.lighthouselabs.org.uk/

The Glasgow Lighthouse Lab is supplying diagnostic services for the UK’s COVID-19 testing service. The Lighthouse Lab is led by the University of Glasgow and is located at the city’s Queen Elizabeth University Hospital Campus. The Glasgow facility is supported by the Scottish Government, BioAscent and the University of Dundee.

https://www.lighthouselabs.org.uk/

The Milton Keynes Lighthouse Lab, set up to provide diagnostic services for COVID-19 testing is based at and managed by UK Biocentre – the largest facility in the UK for storing and processing biological samples.

https://www.lighthouselabs.org.uk/

The UK Lighthouse Labs have been established across the nation in a matter of weeks to dramatically increase the number of coronavirus tests that can take place each day to support the national effort against the coronavirus pandemic.

The new Lighthouse Labs have been constructed through a partnership with the Department of Health, Medicines Discovery Catapult, UK Biocentre and the University of Glasgow. Their development is being closely supported by both the NHS and Public Health England.

COVID-19 swab samples are sent to the laboratories from across the country for analysis. Samples are received from the NHS on the front line and other testing sites, such as the temporary COVID-19 drive-through testing centres.

Lighthouse Labs are based at:

• Alderley Edge, Cheshire
• Cambridge
• Glagow
• Milton Keynes

https://www.lighthouselabs.org.uk/

Contributors:

Leading the sequencing initiative at UCL are:

• Professor Judith Breuer, Professor of Virology
• Dr Sergi Castellano Hereza, Reader in Genomics
• Dr Rachel Williams, Pathogen Genomics Unit Manager
• Dr Mark Kristiansen, UCL Genomics Facility Manager

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.

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/

The University Hospitals Coventry and Warwickshire NHS Trust (UHCW) Blood Sciences Genomics Laboratory,  are working in partnership with University of Warwick to sequence SARS-CoV-2 samples from patients in Coventry and Warwickshire as part of the COG-UK consortium.

Contributors:

• Dimitris Grammatopoulos; Professor Consultant in Molecular Medicine, Blood Sciences Genomics Laboratory, UHCW Pathology
• Sarojini Pandey; Senior Biomedical Scientist Blood Sciences Genomics Laboratory, UHCW Pathology

https://www.uhcw.nhs.uk/

Contributors:

• Professor Nick Loman, Institute of Microbiology and Infection
• Dr Josh Quick, UKRI Future Leaders Fellow, Institute of Microbiology and Infection
• Dr Claire McMurray, Research Fellow (Molecular Biology)
• Dr Sam Nicholls, Research Fellow (Bioinformatics)
• Radoslaw Poplawski, CLIMB System Manager
• Dr Will Rowe, Research Fellow (Bioinformatics)
• Dr Jo Stockton, Research Fellow (Sequencing)

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

Contributors:

• Professor Julian Parkhill, Department of Veterinary Medicine
• Professor Gordon Dougan, Department of Medicine
• Professor Ian Goodfellow, Division of Virology, Department of Pathology
• Dr Luke W Meredith, Division of Virology, Department of Pathology
• Dr M. Estée Török, Department of Medicine
• Dr Myra Hosmillo, Division of Virology, Department of Pathology
• Dr William L. Hamilton, Cambridge University Hospital NHS Foundation Trust
• Dr Martin D. Curran, Public Health England; Cambridge University Hospital NHS Foundation Trust
• Theresa Feltwell, Department of Medicine
• Grant Hall, Division of Virology, Department of Pathology
• Anna Yakovleva, Division of Virology, Department of Pathology
• Fahad A Khokhar, Department of Medicine
• Dr Charlotte J. Houldcroft, Department of Medicine
• Dr Laura G Caller, Division of Virology, Department of Pathology; Francis Crick Institute
• Dr Anna A Smielewska, Department of Pathology
• Dr Aminu S. Jahun, Division of Virology, Department of Pathology
• Dr Sarah L. Caddy, Cambridge Institute for Therapeutic Immunology and Infectious Disease

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

Contributors:

• Professor Andrew Rambaut, Institute of Evolutionary Biology in the School of Biological Sciences
• Dr Kate Templeton, Consultant Clinical Scientist, RIE and Honorary Senior Lecturer in Medical Microbiology
• Dr Thomas Williams, Institute of Genetics and Molecular Medicine

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

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/

Contributors:

• Professor Julian Hiscox, Chair in Infection and Global Health, Institute of Infection and Global Health
• Professor Alistair Darby, Principal Investigator and Co-Director of the Centre for Genomic Research, Institute of Integrative Biology
• Professor Steve Paterson, Professor of Genetics, Institute of Integrative Biology

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

Contributors:

• Dr Darren Smith, Associate Professor in Bacteriophage Biology, Department of Applied Biology, Cellular and Molecular Sciences/Microbiology Group, University of Northumbria
• Dr Andrew Nelson, NU-OMICS laboratory manager and Senior Lecturer, Northumbria University.
• Dr Matthew Bashton, Lead Bioinformatician, Vice Chancellors Fellow- HBBE, Northumbria University.
• Dr Greg Young, HBBE, Northumbria University.
• Members of the research team:  Dr Wen Chyin Yew, Dr Josh Loh, Dr John Allan, Dr Giles Holt, Dr Mohammad A. Tariq (Quadram Institute), Prof. Gary Black, Dr Lynn Dover

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

The team is working in partnership with:

Newcastle Hospitals NHS Foundation Trust: Consultant Virologists Yusri Taha (Clinical Lead), Shirelle Burton-Fanning, Sheila Waugh, Brendan Payne and Microbiology laboratories,  Jennifer Collins and Gary Eltringham.

South Tees Hospitals NHS Foundation Trust: Consultant and Clinical Lead, Paul Baker, James Cook University Hospital Pathology Laboratories and Research, Steven Liggett and Sarah Essex.

North Cumbria Integrated Care NHS Foundation Trust: Consultant Microbiologists Clive Graham (Clinical Lead) and Edward Barton, Laboratory Manager Debra Padgett and Garren Scott

North Tees and Hartlepool NHS Foundation Trust: Associate Director of Durham Tees Valley Research Alliance Jane Greenaway and Senior Biomedical Scientist Emma Swindells.

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

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/

Contributors:

• Professor Oliver Pybus, Department of Zoology
• Professor David Aanensen, Centre for Genomic Pathogen Surveillance, cohosted at the Big Data Institute
• Dr David Bonsall, Nuffield Department of Medicine
• Dr Mariateresa de Cesare, Wellcome Centre Human Genetics
• Professor Julian Knight, Wellcome Centre Human Genetics
• Professor John Todd, Wellcome Centre Human Genetics
• Dr Tanya Golubchik, Big Data Institute
• Professor Dominic Kwiatkowski, Big Data Institute

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

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/

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/

The University of Warwick is working in partnership with The University Hospitals Coventry and Warwickshire NHS Trust (UHCW) Blood Sciences Genomics Laboratory to sequence SARS-CoV-2 samples from patients in Coventry and Warwickshire  as part of the COG-UK consortium.

Contributors:

• Sascha Ott, Associate Professor (Reader) Director, Bioinformatics Research Technology Platform, Dept of Statistics
  
• Dr Meera Unnikrishnan, Associate Professor in Molecular Bacteriology, Warwick Medical School
• Dr Chrystala Constantinidou, Associate Professor in Microbiology, Warwick Medical School
• Dimitris Grammatopoulos, Professor of Molecular Medicine, Warwick Medical School

The following researchers are contributing to the day-to day running of the project:

Sequencing

• Jeff Cheng– PhD Student
• Lucy Frost -PhD student
• Grace Taylor-Joyce -PhD student
• Hannah Bridgewater – Postdoc

Bioinformatics

• Dr Richard Stark
• Dr Laura Baxter

https://warwick.ac.uk/

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/

Contributors:

• Professor Rory Gunson, Consultant Clinical Scientist
• Dr Alasdair MacLean, Clinical Scientist

Working with the MRC-University of Glasgow Centre for Virus Research

https://www.nhsggc.org.uk/about-us/professional-support-sites/laboratory-medicine/laboratory-disciplines/microbiology-and-virology/west-of-scotland-specialist-virology-centre/