COG-UK Table of contents

Foreword

Table of contents

Introduction to the exhibition

Setting the scene

COG-UK and Pathogen genomic surveillance

Whole genome sequencing

Genomic surveillance

COG-UK’s collaborative model

Capturing the human endeavour behind COG-UK

The early days of uncertainty and unease

Scale and seriousness of new disease begins to hit home

Effect starts to be felt at clinical level in the UK

Growing sense of urgency and foreboding

Sowing the seeds for COG-UK

Historical foundations: Pathogen genomic surveillance

UK: The cradle of genomics

High-throughput sequencing technologies

The path to the ARTIC network

Adapting the ARTIC protocol for the SARS-CoV-2 virus

CLIMB

The AMPHEUS platform

MalariaGEN

Genomic surveillance for antimicrobial resistance

Hospital acquired infections

Setting up COG-UK

Sharon Peacock gets the ball rolling

First meeting: COG-UK inauguration

Adopting a mixed model for sequencing

Getting funding and support

Funding awarded

COG-UK’s hub gets moving

Early COG-UK management team

Financing the work

Pulling everyone together

Developing an administrative structure for COG-UK

Broad partnership from the bottom up

Working groups

Network support mechanisms

Consortium Agreement

Rolling out the academic sequencing network

The distributed sequencing model

Sourcing samples

Academic laboratories

University of Glasgow

University of Edinburgh

University of Sheffield

University of Cambridge

University of Portsmouth

University of Exeter

University College London

Quadram Institute

University of Nottingham

University of Northumbria

Queens University Belfast

Public health and NHS laboratories as key partners in COG-UKs sequencing network

Public Health England

PHE Laboratory, Colindale

PHE regional laboratories

Public Health Wales laboratories

Public Health Scotland

Northern Ireland Public Health Agency

NHS laboratories

Barts Health NHS Trust

University College London Hospitals NHS Foundation Trust

The Wellcome Sanger Institute becomes the central sequencing hub

The Wellcome Sanger Institute starts to discuss plans for sequencing COVID-19

The Sanger Institutes role within COG-UK begins to take shape

The Sanger Institute puts in place its sequencing operation

Pillar 2 samples come on board

Storage challenges

Automation

Building the end-to-end sequencing process pipeline

Streamlining the process

SARS-CoV-2 genomes sequenced at Sanger Institute

Sequencing samples - COG-UKs key ingredient

Sample types and format

Condition of samples on arrival

Logistics and transport issues

Sampling framework

Storage and destruction

Sequencing technology

Sequencing capacity

The challenge of data linkage, analysis and visualisation

Drinking from the firehose

Patient metadata

Collecting patient data

Data sharing

Data linkage and cleaning

CLIMB and Majora

Metadata Fridays

Pangolin lineage system - naming lineages

Microreact - visualising data

Civet

Variants of concern - the turning point

Mutations

D614G mutation

N439K

Alpha

Pressure intensifies

The double-edged sword

Learning curve

Single gene target failure

Subsequent variants of concern

Mutation Explorer Dashboard

The human stories of sequencing in lockdown

Motivation for getting involved

Juggling daily life with COG-UK work

Workload

Staff capacity

Laboratory work

Supply shortages

Communication and impact

SAGE Report

Coverage reports

Public and consortium engagement

Media attention

Women in COG

The international dimension

UK - early world leader in SARS-CoV-2 sequencing

Africa

Genomic sequencing around the world

COG-UKs support for other countries

COG-Train

COG-UK research collaborations

COG-UK HOCI study

GenOMICC study

Wastewater samples

The legacy of COG-UK

Team science

Genomic surveillance for public health

Expertise and equipment

Personal impact

Going forward

Appendix 1: Interview transcripts

Appendix 2: COG-UK Together event slides

Appendix 3: COG-UK SAGE Reports

Appendix 4: COG-UK Coverage Reports

Appendix 5: COG-UK blog posts

Appendix 6: Database of tweets around COG-UK

Appendix 7: Snapshots of women in COG

Appendix 8: CLIMB data

Timeline of events around COG-UK

Acknowledgements

Glossary

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