About the COVID-19 Genomics 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/

Wellcome Sanger Institute

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

 

Partners

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

Barking, Havering and Redbridge University Hospitals NHS Trust

Contributor:

https://www.bhrhospitals.nhs.uk/

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/

Betsi Cadwaladr University Health Board

Contributor:

  • Dr Helen Adams

https://bcuhb.nhs.wales/

Big Data Institute

Contributors:

https://www.bdi.ox.ac.uk/

Cambridge University Hospitals NHS Foundation Trust

Contributors:

https://www.cuh.nhs.uk/

Cardiff and Vale University Health Board

Contributors:

http://www.cardiffandvaleuhb.wales.nhs.uk/

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/

County Durham and Darlington NHS Foundation Trust

Contributors:

  • Dr Veena Raviprakash, Consultant Microbiologist
  • Sharon Campbell, Head Biomedical Scientist in microbiology at the University Hospital of North Durham
  • Nicola Sherriff, Senior Biomedical Scientist

https://www.cddft.nhs.uk/

East Kent Hospitals University NHS Foundation Trust

Contributor:

https://www.ekhuft.nhs.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/

Gloucestershire Hospitals NHS Foundation Trust

Contributor:

  • Dr John Boyes, Consultant Medical Microbiologist and Head of Microbiology Department at Gloucestershire Hospitals NHS Foundation Trust; and Honorary Clinical Lecturer, Faculty of Health Sciences, University of Bristol

https://www.gloshospitals.nhs.uk/

Great Ormond Street Hospital for Children NHS Foundation Trust

Contributors:

https://www.gosh.nhs.uk/

Guy’s and St Thomas’ NHS Foundation Trust

Guy’s and St Thomas’ is among the UK’s busiest and most successful NHS foundation trusts. We provide a full range of hospital and community services for people in Lambeth, Southwark and Lewisham, as well as specialist care for patients from further afield including cancer, renal, orthopaedic and cardiovascular services.

  • Ms Chloe L Fisher, Sequencing and analysis, Genomics Innovation Unit, Guy’s and St. Thomas’ NHS Foundation Trust
  • Dr Luke B Snell, Metadata curation, Centre for Clinical Infection & Diagnostics Research (St. Thomas’ Hospital); King’s College London [Researchgate]
  • Mr Adrian W Signell, Sequencing and analysis, Department of Infectious Diseases, King’s College London [ORCID]
  • Dr Gilberto Betancor, Sequencing and analysis, Department of Infectious Diseases, King’s College London [ORCID]
  • Mr Harry D Wilson, Sequencing and analysis, Department of Infectious Diseases, King’s College London [ORCID]
  • Ms Adela Alcolea-Medina, Samples and logistics, Guy’s and St. Thomas’ Hospitals, Viapath [LinkedIN]
  • Ms Themoula Charalampous, Samples and logistics, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [ORCID]
  • Dr Gaia Nebbia, Sequencing and analysis, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Researchgate]
  • Dr Rahul Batra, Project administration, Samples and logistics, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Researchgate]
  • Dr Jonathan Edgeworth, Leadership and supervision – Funding acquisition, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Profile]
  • Dr Ali R Awan, Leadership and supervision – Sequencing and analysis, Funding acquisition, Software and analysis tools Genomics Innovation Unit, Guy’s and St. Thomas’ NHS Foundation Trust [ORCID]

https://www.guysandstthomas.nhs.uk

Health Services Laboratories

Health Services Laboratories is a partnership between The Doctors Laboratory, Royal Free London NHS Foundation Trust (the Royal Free London) and University College London Hospitals NHS Foundation Trust (UCLH).

Contributors:

https://www.hslpathology.com/

Imperial College Healthcare NHS Trust

Contributors:

https://www.imperial.nhs.uk/

Imperial College London

Contributors:

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

Kettering General Hospital NHS Foundation Trust

Contributor:

  • Dr Sahar Eldirdiri, Consultant Microbiologist

https://www.kgh.nhs.uk/

King's College London

Contributors:

  • Dr Rocio Martinez-Nunez, Lecturer in the School of Immunology & Microbial Sciences [Laboratory Page] [Profile]
  • Dr Luke B Snell, Metadata curation, Centre for Clinical Infection & Diagnostics Research (St. Thomas’ Hospital); King’s College London [Researchgate]
  • Mr Adrian W Signell, Sequencing and analysis, Department of Infectious Diseases, King’s College London [ORCID]
  • Dr Gilberto Betancor, Sequencing and analysis, Department of Infectious Diseases, King’s College London [ORCID]
  • Mr Harry D Wilson, Sequencing and analysis, Department of Infectious Diseases, King’s College London[ORCID]
  • Ms Adela Alcolea-Medina, Samples and logistics, Guy’s and St. Thomas’ Hospitals, Viapath [LinkedIN]
  • Ms Themoula Charalampous, Samples and logistics, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [ORCID]
  • Dr Gaia Nebbia, Sequencing and analysis Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Researchgate]
  • Dr Rahul Batra, Project administration, Samples and logistics, Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Researchgate]
  • Dr Jonathan Edgeworth, Leadership and supervision – Funding acquisition,
    Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, Guy’s and St Thomas’ NHS Foundation Trust; King’s College London [Profile]

https://www.kcl.ac.uk/

London School of Hygiene and Tropical Medicine

Maidstone and Tunbridge Wells NHS Trust

Contributor:

  • Dr Graciela Sluga, Deputy Director Infection Prevention and Control & Consultant Microbiologist

https://www.mtw.nhs.uk/

Manchester University NHS Foundation Trust

Contributors:

  • Dr Ryan George, Clinical Scientist/Infection Prevention & Control Senior Surveillance Officer [Researchgate]
  • Dr Nicholas Machin, Consultant Virologist and Clinical Lead for Virology at Manchester University Foundation Trust and Public Health Laboratory Manchester [LinkedIN]
  • Dr Shazaad Ahmad, Consultant Virologist based within the Manchester University NHS Foundation Trust’s Manchester Medical Microbiology Partnership and Public Health England

https://mft.nhs.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/

Newcastle upon Tyne Hospitals NHS Foundation Trust

Contributors:

https://www.newcastle-hospitals.org.uk/

NHS Hampshire Hospitals NHS Foundation Trust

Contributors:

https://www.hampshirehospitals.nhs.uk/

NHS Lothian

Contributors:

https://www.nhslothian.scot/

NIHR Health Protection Research Unit in Healthcare Associated Infections (HCAI) and Antimicrobial Resistance (AMR) at Imperial College

Contributors:

https://www.imperial.ac.uk/medicine/hpru-amr/

Norfolk and Norwich University Hospitals NHS Foundation Trust

Contributor:

http://www.nnuh.nhs.uk/

North Cumbria Integrated Care NHS Foundation Trust

Contributors:

https://www.ncic.nhs.uk/

North Tees and Hartlepool NHS Foundation Trust

Contributors:

  • Jane Greenaway, Associate Director of Durham Tees Valley Research Alliance
  • Emma Swindells, Senior Biomedical Scientist

https://www.nth.nhs.uk/

Northern Lincolnshire and Goole NHS Foundation Trust

Contributors:

  • Dr Tim Sloan, Clinical Associate Professor in Microbiology at University of Nottingham and Honorary Consultant Microbiologist [LinkedIN]
  • Dr Nichola Duckworth, Specialist Biomedical Scientist, Microbiology, Virology
  • Dr Sarah Walsh,

https://www.nlg.nhs.uk/

Oxford University Hospitals NHS Foundation Trust

Contributors:

https://www.ouh.nhs.uk/

Portsmouth Hospitals NHS Trust

Contributors:

https://www.porthosp.nhs.uk/

Princess Alexandra Hospital NHS Trust

Contributor:

https://www.pah.nhs.uk/

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 England, Clinical Microbiology and Public Health Laboratory, Cambridge, UK

Contributors:

https://www.cuh.nhs.uk/addenbrookes-hospital/services/clinical-microbiology-and-public-health-laboratory

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

Contributors:

https://www.qub.ac.uk

Royal Devon & Exeter NHS Foundation Trust

Exeter Clinical Laboratory International is an NHS laboratory located at the Royal Devon and Exeter Hospital in collaboration with the University of Exeter.

Contributors:

 

https://www.rdehospital.nhs.uk/

Royal Free London NHS Foundation Trust

Contributors:

https://www.royalfree.nhs.uk/

Sheffield Teaching Hospitals NHS Foundation Trust

Contributors:

https://www.sth.nhs.uk/

South Tees Hospitals NHS Foundation Trust

Contributors:

https://www.southtees.nhs.uk/

Swansea University

Contributor:

https://www.swansea.ac.uk/

The Centre for Genomic Pathogen Surveillance

Contributors:

https://www.pathogensurveillance.net/

The Leeds Teaching Hospitals NHS Trust

Contributors:

  • Dr Anthony Hale, National Infection Service, Public Health England, and Leeds Teaching Hospitals Trust [Researchgate]
  • Dr Louissa MacFarlane-Smith, National Infection Service, Public Health England, and Leeds Teaching Hospitals Trust [Researchgate]
  • Katherine Harper, National Infection Service, Public Health England, and Leeds Teaching Hospitals Trust

https://www.leedsth.nhs.uk/

UK Biocentre

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:

https://www.ukbiocentre.com/

UK Lighthouse Lab - Alderley Park, Cheshire

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/

UK Lighthouse Lab - Cambridge

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/

UK Lighthouse Lab - Glasgow

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/

UK Lighthouse Lab - Milton Keynes

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/

UK Lighthouse Labs Network

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/

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 Hospitals Birmingham

Contributors:

  • Dr Husam Osman, Consultant Virologist at Heartlands Hospital, University Hospitals Birmingham and Public Health England [LinkedIN]
  • Dr Anna Casey, Queen Elizabeth Hospital, University Hospitals Birmingham [Profile] [Researchgate]
  • Dr Andrew Bosworth, Clinical Virologist at Heartlands Hospital, University Hospitals Birmingham and Public Health England [LinkedIN]
  • Dr Esther Robinson, at Heartlands Hospital, University Hospitals Birmingham and Public Health England [GoogleScholar]
  • Dr Venkat Sivaprakasan, at Heartlands Hospital, University Hospitals Birmingham

https://www.uhb.nhs.uk/home.htm

University Hospitals Coventry & Warwickshire NHS Trust (UHCW NHS Trust)

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:

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

University Hospitals of Leicester NHS Trust

Contributors:

https://www.leicestershospitals.nhs.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 Brighton

Contributors:

https://www.brighton.ac.uk/

University of Cambridge

Contributors:

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

University of East Anglia

University of Edinburgh

Contributors:

School of Biological Sciences

 

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

University of Exeter

Contributors:

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

Contributors:

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/

University of Nottingham

Contributors:

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.

Deep Seq

Deep Seq is the University of Nottingham Next Generation Sequencing Facility in the Life Sciences, Queens Medical Centre. Deep Seq is able to help with projects from both within and outside the University.

Deep Seq Team:

Clinical Microbiology

Virology

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

University of Oxford

Contributors:

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

University of Portsmouth

Contributors:

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 [ORCID] [Profile]
  • Dr Matthew Parker, Sheffield Bioinformatics Core at the National Institute of Health Research (NIHR) Sheffield Biomedical Research Centre [ORCID] [Profile]

Members of the research team:

The team is working in partnership with:

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

University of Surrey

Contributors:

https://www.surrey.ac.uk/

University of Warwick 

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:

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

Sequencing

Bioinformatics RTP

https://warwick.ac.uk/

Wellcome Centre for Human Genetics

Contributors:

https://www.well.ox.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 Jeffrey Barrett, 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 more than 300 contributors can be seen here: https://www.sanger.ac.uk/covid-team

Including:

 

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

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

Contributors:

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/

Wye Valley NHS Trust

Contributors:

https://www.wyevalley.nhs.uk/

Core management team 

Professor Sharon Peacock, Executive Director and Chair

Leadership Team

Professor Sharon Peacock CBE FMedSci is Executive Director and Chair at COG-UK, and a Professor of Public Health and Microbiology in the Department of Medicine at the University of Cambridge. She is a world authority on pathogen genomics, antibiotic resistance, and a range of specific infectious pathogens. This includes Staphylococcus aureus (including MRSA), and Burkholderia pseudomallei (the cause of the tropical infectious disease, melioidosis). Professor Peacock is a non-executive director at Cambridge University Hospitals NHS Foundation Trust, and holds a secondment with Public Health England (PHE) as Director of Science (Pathogen Genomics).

 

Dr Katerina Galai, Associate Director

Leadership Team

Dr Katerina Galai is Associate Director for COG UK, heading up communications, governance, strategic planning, legal and financial functions. She is a multidisciplinary scholar with research expertise in international law and cross-sector business experience. Before joining COG-UK, Katerina spent three years at RAND Europe developing a portfolio of qualitative research methods and working on a number of UK and European research projects delivering analysis, impact and recommendations to senior policy makers. She is a UK expert on the use and regulation of private military companies and she recently published a monograph with Routledge on the topic.

 

Beth Blane, Logistics Manager

Logistics 

Beth Blane is the Logistics Manager at COG-UK. She is also a Laboratory Manager in the Department of Medicine at the University of Cambridge, and has been since 2012. Beth is a Health and Care Professions Council registered Biomedical Scientist, and previously worked in the clinical microbiology lab at Addenbrooke’s Hospital, Cambridge. She has worked on a range of projects including the surveillance of carriage and transmission of healthcare-associated bacteria in a long-term health facility, the study of nasal carriage of Staphylococcus aureus, and most recently the implementation of real-time whole genome sequencing of MRSA in a clinical setting.

 

 Dr Andrew Jermy, External Communications Advisor

Communications

Dr Andrew Jermy has been working with COG-UK since March 2020 to prepare reports for the Consortium as External Communications Lead. Andrew gained his PhD in Molecular Biology from the University of Manchester, UK, studying fungal protein trafficking and secretion. He subsequently spent more than a decade as a professional microbiology editor for various journals, including Nature Reviews Microbiology, Nature and was the Chief Editor for the launch of Nature Microbiology in 2015. In February 2019, Andrew left Nature to launch Germinate Science Consulting to deliver editorial, writing and communications services directly to the research community, through which he supports COG-UK.

 

Ellena Brooks, Administrator

Administration 

Ellena Brooks is an Administrator for the Operations team at COG-UK. They came to the organisation through the Department of Medicine at the University of Cambridge, having previously worked as a Research Centre Coordinator for the university’s Department of Psychology.

 

Dr Nazreen Hadjirin, Project Support

Research / Administration 

Dr Nazreen Hadjirin is currently providing project support to COG-UK, after joining the University of Cambridge as a Postdoctoral Research Associate in 2020. She obtained her PhD in microbial genomics at the Department of Veterinary Medicine, University of Cambridge, under the supervision of Professor Mark Holmes. She had post-doctoral training under Dr Lucy Weinert in evolutionary genomics also at the Department of Veterinary Medicine. Her research interests include antimicrobial resistance in zoonotic pathogens, host pathogen adaptations and microbial genomics.

 

Dr Dinesh Aggarwal, Infectious Diseases and Microbiology Specialist Trainee

Research 

Dr Dinesh Aggarwal is currently working at COG-UK and Public Health England to characterise SARS-CoV-2 importations, and has a special interest in transmission within care homes and universities as part of the Cambridge University Screening Study. Dinesh completed his medical degree from UCL and the University of Cambridge in 2013. He is an Infectious Diseases and Microbiology Specialist Trainee in the London Deanery and was awarded a Wellcome Clinical PhD Fellowship in 2020 to understand the biological basis of Staphylococcus aureus carriage under the supervision of Professor Peacock, Professor Danesh and Dr Harrison at The University of Cambridge and the Wellcome Sanger Institute.

Dr Ewan Harrison, Director of Strategy and Transformation

Leadership Team

Dr Ewan Harrison is Director of Strategy and Transformation at COG-UK, Career Development Fellow at the Wellcome Sanger Institute, and a Senior Research Associate at the Department of Medicine and Honorary Senior Fellow in the Department of Public Health and Primary Care, both at the University of Cambridge. He completed his PhD at the University of Leicester on the genomics and pathogenesis of Pseudomonas aeruginosa in 2009, supported by a Medical Research Council Studentship. His post-doctoral work at the University of Cambridge focused on the analysis of MRSA populations in animals and humans and tracking the transmission of MRSA in healthcare facilities.

 

Dr Catherine Ludden, Director of Operations

Leadership Team

Dr Catherine Ludden is Director of Operations at COG-UK, and is responsible for overseeing COG-UK operations, developing long-term operational strategies, coordinating public health investigations, and engaging with technical experts, collaborators and senior leaders. Catherine is a genomic epidemiologist with expertise in pathogen genomics, antibiotic resistance, and clinical microbiology. Prior to joining COG-UK, Catherine was working with the European Centre for Disease Prevention and Control where she provided scientific and technical expertise for the analysis and interpretation of European whole genome sequencing datasets and supported international outbreak investigations. She is a One Heath expert and was previously awarded a Sir Henry Postdoctoral Wellcome Fellowship at the London School of Hygiene and Tropical Medicine to define reservoirs and transmission of antimicrobial-resistant Escherichia coli using a One Health approach.

 

Theresa Feltwell, Logistic Assistant

Logistics 

Theresa Feltwell is currently assisting COG-UK with logistics support. Prior to this she worked with Dr Estée Török in the Department of Medicine at the University of Cambridge on a project in association with WaterScope. During that time, she was seconded to set up logistics to collect SARS-CoV-2 samples for local sequencing, feeding into infection control surveillance and COG-UK. Theresa had over 20 years’ experience working in microbiology research at the Wellcome Sanger Institute before joining COG-UK. She is currently studying part time for an MSc in Biomedical Science by Distance Learning.

 

Georgie McManus, Communications Officer

Communications

Georgie McManus joined COG-UK as Communications Officer in November 2020, after working in a similar role at the Hudson Institute of Medical Research in Melbourne. Georgie graduated from the University of Birmingham with a degree in Biochemistry, and following this spent three years as a Medical Writer in healthcare communications. She then established her own science writing business before joining COG-UK, through which she led a range of projects within the medical research and healthcare communication sectors.

 

Kim Smith, Administrator

Administration 

Kim Smith joined COG-UK in October 2020 as an Administrator. Before joining COG-UK, Kim gained experience within event coordination and previously worked within Health Education. Her experience includes logistical and administrative organisation, communications, project and budget planning.

 

Alessandro Maria Carabelli, Postdoctoral Research Associate

Research 

Dr Alessandro Maria Carabelli is a Postdoctoral Research Associate at COG-UK, currently focusing on the detection of SARS-CoV-2 mutations for public health benefit, coordinating and working closely with an interdisciplinary team at the Consortium (Mutational Analysis and Tracking working group). He joined the University of Cambridge, Department of Medicine as a Research Associate in 2020. His PhD was undertaken at Nottingham University, under the supervision of Professor Paul Williams. This focused on the physical microbiology of polymers that are resistant to bacterial attachment, and explored the biological-material interface using an interdisciplinary approach.

Principal Investigators (PIs)

Professor Andrew Rambaut

University of Edinburgh 

Professor Andrew Rambaut, FRSE, is a Professor of Molecular Evolution at the University of Edinburgh. After gaining his BSc in Zoology from the University of Edinburgh and then his PhD in Zoology from University of Oxford in 1997, Professor Andrew Rambaut remained at Oxford until 2006. He then took up the Royal Society University Research Fellowship position and became Chair of Molecular Evolution in 2010. His research is focused on evolutionary and epidemiological study of viral pathogens of humans and animals. He is interested in the evolution of emerging human viral pathogens including Ebola, Zika and Influenza viruses.

 

Dr David Simpson 

Queen’s University Belfast

Dr David Simpson is a Reader in the School of Medicine, Dentistry and Biomedical Sciences at Queen’s University Belfast. His research applies molecular biology and bioinformatics to study vision and cardiovascular diseases. The aim of his research is to provide a better understanding of the causes of eye and vascular diseases. This is achieved by application of advanced molecular biology approaches to provide novel insights, enabling both development of new treatments and design of improved diagnostic and prognostic tests. He is Academic lead of the Queen’s Genomics Core Technology Unit and has applied his experience with nanopore sequencing to support rapid turnaround of SARS-CoV-2 sequences within the Belfast COG-UK hub. He is also applying a miniaturised library preparation protocol to facilitate high throughput SARS-CoV-2 sequencing on the Illumina platform.

 

Professor Emma Thompson

University of Glasgow

Professor Emma Thompson, OBE, is a Professor in Infectious Diseases at the MRC-University of Glasgow Centre for Virus Research. She was recently awarded Officer of the Most Excellent Order of the British Empire (OBE) for services to the NHS during the COVID-19 response. Currently Professor Thomson is heavily involved in sequencing SARS-CoV-2 as it circulates in the UK as part of COG-UK. She is the local principal investigator for two vaccine trials running within Greater Glasgow and Clyde. In addition to her work with COVID-19, Professor Thomson’s main research focus is on emerging infections in Uganda, working closely with the Uganda Virus Research Institute and in the UK.

 

Dr Jeffrey Barrett

Wellcome Sanger Institute

Jeff is leading the Wellcome Sanger Institute’s Covid-19 genomic surveillance programme, and its contribution to COG-UK. The programme sequences and analyses samples from positive community (pillar 2) tests around the UK to help detect outbreaks and monitor for mutations that might affect vaccine efficacy. Prior to that Jeff studied the genetic basis of human diseases in both industry and academia. Most recently he was Chief Scientific Officer at Genomics plc, and before that Director of Open Targets, a public-private initiative to use human genetics to improve early stage drug discovery. He was a group leader at the Sanger Institute for ten years, where he focused on the genetics of inflammatory and immune diseases. He is a Fellow of the Academy of Medical Sciences.

 

Professor Judith Breuer

University College London

Professor Judith Breuer is a Professor of Virology at University College London. Research in her lab focuses on the application of next generation sequencing and phylogenetics to virus diagnostics and discovery. Her laboratory has pioneered whole pathogen genome sequencing directly from clinical material using targeted enrichment methods which obviate the need for prior amplification by culture or PCR, and have established the method as an automated high-throughput pipeline with associated bioinformatics. Her lab at Great Ormond Street were the first in the UK to introduce metagenomics for the identification of viruses in cases of encephalitis and are now using this routinely on many speciments.  Professor Breuer is PI on Wellcome trust collaborative award exporing why noroviruses cause pandemics. She is Chief Investigator of the COG-UK Hospital Onset COVID-19 Infections (HOCI) study.

 

Professor Matt Loose

University of Nottingham

Professor Matt Loose is based at the School of Life Sciences, University of Nottingham. A developmental biologist and bioinformatician, he heads up DeepSeq, the University of Nottingham next-generation sequencing platform. The DeepSeq lab is equipped with a range of sequencing platforms and provides services for research and industry. Matt has developed a range of tools for long read sequencing including, most recently, adaptive sampling which enables nanopore sequencers to choose which bits of a genome to sequence as they go. Matt leads the Nottingham COG-UK team and is supported by the local virology teams.

 

Professor Oliver Pybus 

University of Oxford

Professor Oliver Pybus is a Professor of Evolution and Infectious Disease in the Department of Zoology at the University of Oxford. He investigates the evolutionary and ecological dynamics of infectious diseases, particularly rapidly-evolving viruses. He also develops new methods of genetic analysis based on phylogenetic, phylodynamic and population genetic theory. Professor Pybus is a Professorial Fellow of New College at the University of Oxford and a Co-Director of the Oxford Martin School Programme on Pandemic Genomics. He is a Chief Editor of the open access journal Virus Evolution, and holds a Professorship at the Royal Veterinary College. Professor Pybus and his team are (i) analysing the genetic lineage structure of the SARS-CoV-2 infection in the UK, (ii) quantifying the international movement and importation of virus lineages, and (iii) investigation the dynamics and evolution of virus mutations.

 

 

Dr Thushan de Silva

University of Sheffield

Dr Thushan de Silva is a Senior Clinical Lecturer at the University of Sheffield, in the Academic Clinical Infection Group in the Department of Infection, Immunity and Cardiovascular Disease. He has been an Honorary Consultant Physician in Infectious Diseases at the South Yorkshire Regional Department of Infection and Tropical Medicine in Sheffield since 2016. He also continues to be a Visiting Scientist and Principal Investigator in the Vaccines and Immunity Theme at the MRC Unit The Gambia at London School of Hygiene and Tropical Medicine (LSHTM) and is an Honorary Associate Professor at the LSHTM.

Professor Darren Smith 

Northumbria University 

Professor Darren Smith is a Personal Chair in Bacteriophage Biology within the Faculty of Health and Life Sciences, Northumbria University. He directs NU-OMICS the Northumbria University DNA sequencing research facility and is the Microbial Environments theme lead for the Research England Expanding Excellence funded ‘Hub for Biotechnology in the Built Environment (HBBE)’. His research spanning over 2 decades has focussed on the biology of lysogenic bacteriophages and their role in altering bacterial function and fitness linked to chronic infection of the lung and gut. He completed both Degree and PhD at the University of Liverpool. Prior to joining Northumbria University, Professor Smith completed postdoctoral research in both Stx-bacteriophage biology in the University of Liverpool microbiology department and the HIV pharmacology group, moving from Stx-phage biology to the impact of nanoformulation on highly active antiretroviral therapies used in the treatment of HIV infection.

 

Dr Derek Fairley 

Queen’s University Belfast 

Dr Derek Fairley is a Research Scientist at the Belfast Health and Social Care Trust (BHSCT) and an Honorary Lecturer at Queen’s University Belfast (QUB). He is a molecular microbiologist with a particular interest in translational research, diagnostic assay development, and applying modern molecular methods in clinical settings. He is responsible for developing new molecular diagnostic assays for detection, quantification and typing of bacterial and viral pathogens in the Regional Virus Laboratory. He led the regional Clostridium difficile and Pseudomonas aeruginosa molecular typing services for Northern Ireland, and is working to introduce pathogen genomics services for clinical and public health microbiology and virology teams. At COG-UK he is co-ordinating sequencing and analysis work by the Belfast sequencing hub, which is a collaboration between QUB and BHSCT, and provides sequencing coverage for all 5 NHS Trusts and 20 hospitals in Northern Ireland

 

Dr Erik Volz

Imperial College London

Dr Erik Volz is a Senior Lecturer at Imperial College London, in the Faculty of Medicine, School of Public Health where he studies infectious disease dynamics and evolution of pathogens. The aim of this work is to improve surveillance of infectious diseases using genetic data. Applications include outbreak detection, forensics, and forecasting epidemic trends. As part of the UK COVID-19 Genomics Consortium, Dr Volz contributes to analysis of genetic variants, outbreak detection, and modelling for  evaluation of public health interventions.

 

Professor John Danesh

University of Cambridge 

John Danesh is Professor of Epidemiology and Medicine and Head of Department of Public Health and Primary Care at the University of Cambridge, and also Director of the Cambridge site of Health Data Research UK and a Faculty Member of the Wellcome Trust Sanger Institute. He holds a British Heart Foundation Personal Chair and an NIHR Senior Investigator Award. In 2015, he was elected to the Fellowship of the UK Academy of Medical Sciences. He trained in medicine at the University of Otago in New Zealand and at the Royal Melbourne Hospital in Australia, and, as a Rhodes scholar, trained in epidemiology at Oxford University and the London School of Hygiene and Tropical Medicine.

 

Dr Justin O’Grady

Quadram Institute

Dr Justin O’Grady is a Group Leader in the rapid infectious disease and foodborne pathogen diagnosis and detection research group at the Quadram Institute. He joined the Quadram Institute in April 2018 while maintaining his affiliation with the University of East Anglia. His research continues to focus on the molecular diagnosis of pathogens with the aim of translating this research broadly, in different sectors and diseases, to maximise community and patient benefit. He gained his B.Sc. in Microbiology, M.Sc. (Res) in infectious diseases molecular diagnostics and Ph.D. in molecular diagnosis of bacterial pathogens in food all at the National University of Ireland Galway. Dr O’Grady is the PI for the COG-UK Norwich sequencing site, where there is a large team of molecular biologists and bioinformaticians (led by Dr Andrew Page) that provide viral lineage information for hospital cases in Norfolk and parts of Suffolk (pillar 1) and for community cases nationally (pillar 2). They also work closely with PHE and Norfolk Test and Trace to provide rapid outbreak sequencing and analysis for the region.

 

Professor Neil Ferguson 

Imperial College London

Professor Neil Ferguson OBE FMedSci is Director of the Jameel Institute and the Medical Research Council Centre for Global Infectious Disease Analysis at Imperial College London. His research aims to improve understanding of the epidemiological factors and population processes shaping infectious disease spread in human and animal populations. A key practical focus is the analysis and optimisation of intervention strategies aimed at reducing transmission or disease burden. Much of his work is applied, informing disease control policy-making by public and global health institutions.

Dr Sam Robson

University of Portsmouth

Dr Sam Robson is a Senior Research Fellow at the University of Portsmouth, where he is the Faculty Bioinformatics Lead, and Bioinformatics Lead at the Centre for Enzyme Innovation. He collaborates with researchers across the faculty on a number of different projects, in particular those utilising high-throughput next generation sequencing methods. He also helps to identify and develop enzymatic solutions to help solve global environmental issues such as the current plastics crisis. He has been part of the team that has previously identified an enzyme (PETase) able to efficiently catalyse the breakdown of Polyethylene terephthalate (PET) plastics. Following lockdown of University labs in March 2020, Dr Robson’s team worked in partnership with Portsmouth Hospitals University NHS Trust to set up a temporary sequencing facility at their local hospital site for sequence the virus from COVID-19 positive patients. Since then, his team have partnered with the COG-UK consortium to provide whole genome sequencing coverage from NHS sites across the south coast. These data provide essential coverage to the COG UK surveillance program, as well as feeding directly back to infection control measures at partner hospitals.