News and Updates from COG-UK
The COVID-19 Genomics UK (COG-UK) Consortium is creating networks of COVID-19 sampling, genome sequencing and analysis that use new and refined tools and techniques to provide the UK with valuable insights and data on the SARS-CoV-2 virus. Below we list the reports, commentaries and news of the consortium. Additional information is available on our Twitter feed: @CovidGenomicsUK and our LinkedIn page.
COG-UK captures SARS-CoV-2 samples from COVID-19 infections from across the UK. These weekly summaries include information on sequencing coverage (the number of sequences available in COG-UK out of the total number of people with a COVID-19 infection) across Wales, Scotland, England and Northern Ireland. View our latest coverage report here.
For journalists wishing to know more about the COG-19 consortium, please contact: email@example.com
Reports, News, Commentaries and Blogs from COG-UK
Asymptomatic screening and genome sequencing help Cambridge understand spread of SARS-CoV-2 among its students
Since the start of the academic year in October 2020, the University of Cambridge has been offering regular SARS-CoV-2 tests to all students living in its Colleges, even if they show no symptoms. Initial results suggest that the screening programme, together with the University’s public health measures and responsible student behaviour, has helped limit the spread of the virus.
‘World-class’ CLIMB project receives £1.2 million funding boost from UKRI
As part of a wider £213 million investment to expand and upgrade ‘world-class’ research infrastructure, the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project — the ultra-high performance computing infrastructure which has supported the COVID-19 Genomics UK (COG-UK) consortium throughout the pandemic — has received a £1.2 million funding boost from UK Research and Innovation (UKRI).
Watch the first COG-UK Showcase Event
On the 16th December, the COVID-19 Genomics UK (COG-UK) consortium presented its first Showcase Event: SARS-CoV-2 sequencing to inform clinical care, public health interventions and policy decisions. Watch the recording of the event here.
Persistent SARS-CoV-2 infection and viral evolution tracked in an immunocompromised patient
All viruses, including SARS-CoV-2, accumulate mutations as they evolve over time. Most mutations have no detectable effect on the biology of the virus. But a few have the potential to change the virus in minor ways and be spread to other hosts. But what are the drivers of viral evolution, and could antibody treatment have any influence on this process?
A short history of the COVID-19 Genomics UK (COG-UK) Consortium
This short history of the development of the COG-UK consortium is dedicated to everyone who has contributed to its success. As we approach the holiday season, I want to offer my thanks and gratitude for your unlimited energy, enthusiasm, commitment and support.
Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations
The variant described today in the House of Commons contains a novel set of mutations associated with a lineage spreading rapidly in the South East of England (and more widely) that is the subject of ongoing investigations by the UK Public Health Agencies, coordinated by Public Health England and supported by COG-UK. This variant carries a set of mutations including an N501Y mutation in the receptor binding motif of the Spike protein that the virus uses to bind to the human ACE2 receptor.
Two new reports to SAGE on the genomic analysis of epidemic waves of COVID-19 in Scotland and Wales
Two reports submitted to the Scientific Advisory Group for Emergencies (SAGE) describe the genomic history of SARS-CoV-2 in Scotland and Wales throughout the first epidemic wave, and into the second. These provide windows of evidence into the effect of travel and lockdown on the fate of circulating SARS-CoV-2 variants and lineages.
How do we collect and sequence SARS-CoV-2 samples?
As we learn more about COVID-19 and how the virus changes over time, the way we collect and sequence positive SARS-CoV-2 samples will continue to evolve. In this blog we take a look behind the scenes to find out more about our genome sequencing process.
Upcoming COG-UK Showcase Event – 16th Dec 2020
On the afternoon of the 16th of December, the COVID-19 Genomics UK (COG-UK) Consortium will be presenting it’s first ‘Showcase Event’ with three sessions covering some of the major areas of work for COG-UK over the last 8 months, including evidence on SARS-CoV-2 lineage introduction and transmission, an overview of genomics-informed evidence on transmission in specific environments, and mutations and their implications for transmission, disease severity, therapeutics and vaccines.
COG-UK researchers make highly cited list
Eight COG-UK Consortium members and associates have been recognised by Clarivate as some of the most highly cited researchers of 2020.
COVID-19 in care homes — what have we learned from genome sequencing?
Read COG-UK partner Quadram Institute’s explainer blog on the latest findings of how the SARS-CoV-2 virus spreads within care homes.
The value of large-scale coordinated sequencing activities to understand a pandemic in real-time
In recent work from COG-UK consortium investigators, Erik Volz and colleagues investigated the D614G mutation in the population by using more than 25,000 viral genomes that have been sequenced in the UK over a period between February and June 2020 in order to understand the pandemic in real-time.
Priority Research Questions for COG-UK
Professor Sharon Peacock, COG-UK Director, and Professor Ravi Gupta, Wellcome Senior Fellow in Clinical Science at the University of Cambridge, discuss COG-UK's research priorities and how advancements in our scientific understanding of COVID-19 have refreshed the Consortium's thinking.
CLIMB project receives honours for supporting COG-UK alongside other computing teams
HPCwire has presented the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) project, alongside other computing teams across COG-UK, with the Readers’ Best High Performance Computing Collaboration award, after providing COG-UK with vital computing infrastructure and bioinformatics analysis.
What next for COG-UK following new funding of £12.2 million?
Professor Sharon Peacock discusses the new £12.2 million funding from the Department of Health and Social Care Testing Innovation Fund — how the funds will be used and what it means for COG-UK.
The COG-UK Project Hospital-Onset COVID-19 Infections (HOCI) Study
The COG-UK HOCI study aims to evaluate the benefits of rapid COVID-19 genomic sequencing on infection control in preventing the spread of the virus in UK NHS hospitals. 2,000 patients will be recruited to the study at approximately 15 NHS hospitals across the UK. The study is funded by COG-UK and benefits from the extensive network of existing sequencing partners across the UK. COG-UK HOCI is sponsored by University College London (UCL), with Professor Judith Breuer as Chief Investigator.
£12.2 million boost for SARS-CoV-2 real-time genomic surveillance
The COVID-19 Genomics UK (COG-UK) Consortium has been backed by the Department for Health and Social Care Testing Innovation Fund to expand whole genome sequencing of positive SARS-CoV-2 virus samples to map how COVID-19 spreads and evolves. The £12.2M funding will facilitate the genome sequencing capacity needed to meet the increasing numbers of COVID-19 cases expected in the UK this winter.
COG-UK passes 100K genomes
As the 100K mark whizzes by, it is worth reflecting on why this unprecedented viral genomic surveillance effort has been needed, how the genome data generated has been used to better understand the transmission dynamics underpinning the COVID-19 pandemic in the UK, how the same data has provided insights that have helped to inform outbreak responses from the local to national level, and how working collaboratively and in an open manner has been of fundamental importance in getting this far.
SARS-CoV-2 mutations, the science behind the mink case
The Danish government will cull 17 million farmed mink in the country after detecting variants of the SARS-CoV-2 in these animals with mutations that have been transmitted back to humans (corroborating recent reports from the Netherlands Ref 1 and Ref 2). The Danish prime minister described these viral variants as a potentially serious threat for the development of a future vaccine as they allegedly showed resistance to antibodies present in sera from people recovered from infection. However, the supporting evidence for this statement has not yet been provided.
SARS-CoV-2 mutations, what we have learned from new fast-growing lineages and the Spike N439K variant
The combination of epidemiological studies which allow the identification of new variants spreading among communities and experimental work carried on by virology groups, is necessary to fully characterise SARS-CoV-2 mutations and their biological and clinical importance.
Software tool will help doctors identify and prevent hospital transmission of SARS-CoV-2
The software combines knowledge about infection dynamics, data describing the movements of individuals, and genome sequence data to assess whether or not coronavirus has been transmitted between people in the hospital environment.
How a COG-UK Partner is helping to sequence tens of thousands of COVID-19 samples
Read the Wellcome Sanger Insitute's Blog post about their work and watch their video
COG-UK report 12 – 15th October 2020
As of 22nd October, the COVID-19 Genomics UK (COG-UK) Consortium has sequenced more than 81,000 SARS-CoV-2 virus genomes from the UK, representing about 45 per cent of the global total.
Report 12: 15th October 2020 – COVID-19 Genomics UK (COG-UK) Consortium
COG-UK genome sequence data and tools have been used in more than 120 retrospective and live public health outbreak investigations in the UK since March 2020. Analysis of COG-UK and GISAID data highlights the need to establish a systematic approach for monitoring the appearance and spread of all variants of the SARS-CoV-2 virus
Queen honours three COG-UK scientists in 2020 Birthday List
Three scientists from the COVID-19 Genomics UK (COG-UK) consortium, representing research efforts in England, Scotland and Wales, have been honoured by the Queen for their roles in delivering vital services during the first phase of the COVID-19 global pandemic.
COG-UK Researcher honoured by Queen for COVID-19 work
Professor Emma Thomson, Professor in Infectious Diseases at the MRC-University of Glasgow Centre for Virus Research has been recognised in the Queen’s Birthday Honours. She has been awarded an OBE for services to the NHS during the COVID-19 response.
Spread of COVID-19 mapped in hospitals to ‘break the chain’ of transmission
A first-of-its kind clinical trial, led by scientists at UCL, will evaluate the use of ‘real time’ viral genomic data to reduce the spread of COVID-19 within hospitals.
Report 11: 8th September 2020 – COVID-19 Genomics UK (COG-UK) Consortium
Rapid genome sequencing coupled with integration of epidemiological data has enabled the identification of transmission points and informed intervention measures during outbreaks among highly vulnerable patients in renal dialysis units (RDUs) in Scotland and the East of England
Report 10: 11th August 2020 – COVID-19 Genomics UK (COG-UK) Consortium
In just 5 months, COG-UK has sequenced and analysed more than 40K SARS-CoV genomes. Genomic analyses have demonstrated that cases of shock and multisystem inflammation in children positive for SARS-CoV-2 are not associated with specific polymorphisms in any viral gene
COG-UK report 9 - 25th June 2020
The COVID-19 Genomics UK (COG-UK) Consortium has now sequenced more than 32,000 SARS-CoV-2 virus genomes from the UK. In the 9th report from the Consortium, dated 25th June, 29,593 of these were analysed
Supplementary Report: 28th June 2020 – Report on use of SARS-CoV-2 genomics to understand transmission
This paper supplements 9 reports submitted to SAGE in the last 3 months, which are available on the COG-UK website https://www.cogconsortium.uk
Report 9: 25th June 2020 - Report COVID-19 Genomics UK (COG-UK) Consortium
COG-UK has sequenced more than 29K SARS-CoV-2 genomes during the past 15 weeks and the UK remains by far the single biggest producer of genome data having contributed ~53% of the global total.
Report 8: 11th June 2020 – COVID-19 Genomics UK (COG-UK) Consortium
The scale of the data generated by COG-UK continues to increase weekly, with more that 25K SARSCoV-2 genomes now sequenced, corresponding to ~55% of the global total.
The COVID-19 genome
Information from the genome sequences will help track the spread of the coronavirus in the UK and support public health planning and clinical decision making
COG-UK preliminary analysis reveals the frequency and source of virus introductions into the UK
The latest analysis of the COVID-19 epidemic in the UK combines large-scale data and genomic sequencing to provide a detailed picture of the number and sources of SARS-CoV-2 introductions into the UK
Report 7: 28th May 2020 – COVID-19 Genomics UK (COG-UK) Consortium
With 17 sequencing centres now active, COG-UK has passed a significant milestone by sequencing and analysing more than 20K SARS-CoV-2 genomes to date, corresponding to 56% of the global total number of genomes
Analysis of COVID-19 Genomes reveals large numbers of introductions to the UK in March
The latest COG-UK data reports show large numbers of independent introductions of the virus into the UK . However, recent data suggest new UK COVID-19 cases are arising from local spread.
Report 6: 14th May 2020 – COVID-19 Genomics UK (COG-UK) Consortium
All 15 COG-UK sites are now active and have sequenced and analysed 16,670 SARS-CoV genomes to date. Sequencing capacity now outstrips the availability of samples in some areas owing to the decline of the first wave of infections.
Commentary: COG-UK Report 5, 7th May 2020
The findings highlight the importance of ongoing, larger studies, with additional metadata. Such studies will be vital to study transmission in care settings and inform control strategies
Report 5: 7th May 2020 – COVID-19 Genomics UK (COG-UK) Consortium
A further 4 sequencing centres have joined COG-UK. bringing the total to 14 including the Wellcome Sanger Institute (WSI). The number of SARS-CoV-2 genomes sequenced and analysed to date is 10,843. The UK has reported the largest number of genomes of any individual country in the pandemic to date, accounting for over half of the global total.
The COVID-19 Genomics UK (COG-UK) consortium and the Canadian COVID Genomics Network (CanCOGeN) launch new partnership
By sharing knowledge, lessons learned and protocols, the initiatives will each support national efforts to coordinate the work of healthcare, public, private and academic organisations to sequence and analyse the spread and evolution of the SARS-CoV-2 virus and how it affects patients
A letter to Medical Directors, Consultant Virologist/Microbiologists, Infectious Diseases Physicians, Infection Laboratory Managers in the NHS introducing the project
Downloadable Document for NHS clinicians and managers: Participating in the COVID-19 Genomic UK (COG-UK) Consortium 24 April 2020
Report 4: 16th April 2020 – COVID-19 Genomics UK (COG-UK) Consortium
COG-UK has nine active sequencing centres which combined have sequenced a total of 3202 SARSCoV-2 genomes, which accounts for over one third of the global total. Two predominant long-established SARS-CoV-2 lineages (UK5 and UK17) can be distinguished in genome sequences from across the UK.
Report 3: 9th April 2020 – COVID-19 Genomics UK (COG-UK) Consortium
COG-UK has brought online an additional sequencing centre (Exeter) and increased the number SARSCoV-2 genomes sequenced and analysed to a total of 1679 (up from 806 on the 31st of March). The UK has now reported the largest number of genomes of any individual country in the pandemic to date, accounting for around one third of the global total.
Report 2: 1st April 2020 – COVID-19 Genomics UK (COG-UK) Consortium
COG-UK has brought online an additional sequencing centre (Cambridge) and increased the number SARS-CoV-2 genomes sequenced and analysed to a total of 806 (up from 260 on the 23rd March). The UK has now reported the largest number of genomes of any individual country in the pandemic to date.
Report 1: 23rd March 2020 – COVID-19 Genomics UK (COG-UK) Consortium
The COG-UK consortium has rapidly established a multi-agency national network to deliver coordinated large-scale sequencing and analysis of SARS-CoV-2 genomes. In the space of 12 days, the COG-UK centres already online have sequenced and analysed 260 SARS-CoV-2 genomes.
COG-UK Reports PDF Downloads
The reports generated by the COG-UK consortium are posted on this website. These reports are provided to the four Public Health Agencies and to the UK government to track SARS-CoV-2 evolution in the UK in order to provide epidemiological insights.