COVID-19 Genomics Initiative at the Wellcome Sanger Institute
We provide near real-time monitoring of COVID-19 viruses' genomes in the UK. Our data guide public health actions, and identify changes that could make vaccines less effective
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COVID-19 Surveillance Tool
This website shows how SARS-CoV-2 lineages have changed in frequency over time across England
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COVID-19 surveillance (as of 18 September 2023)
coronavirus genomes sequenced by the Sanger Institute
Sanger staff have contributed to the 7-days-per-week operation
coronavirus genomes sequenced around the globe (GISAID)
How COVID-19 surveillance works
COVID-19 Genomics UK (COG-UK) Protocols
We provide a range of guides on all aspects of large-scale COVID-19 sequencing and monitoring. Our protocols cover the nation-wide collection of samples and metadata, through how to prepare and read the genomes, to the best ways of analysing and visualising the data
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Read our COVID-19 blog
Discover how our scientists contribute to the surveillance effort
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Sanger Seminar: Comprehensive genomic surveillance of SARS-CoV-2 in the UK
Human Cell Atlas COVID-19 research
As part of our work in the Human Cell Atlas initiative, our research teams explore how the SARS-CoV-2 virus enters people’s cells and cause symptoms.
To find out more, please visit: https://www.humancellatlas.org/covid-19/
Latest COVID-19 News and Blogs
26 Jun 2023
Swapping stethoscopes for sequencing - a doctor's journey
Chenqu Suo looks back on her PhD, discussing her scientific highlights and her thoughts about what makes the Sanger Institute a special place to study.
25 Jan 2023
Celebrating the contributions of women during the pandemic
How did the pandemic impact the role of women in science? And what will its legacy be? These were just some of the questions discussed at the Snapshots of Women in COG: Scientific excellence during the COVID-19 pandemic book launch event
20 Jan 2023
Meet Cristina Ariani - Malaria Parasite Surveillance Lead
Combining bold scientific leadership, deep operational expertise, and a knack for building community, Cristina Ariani is ready to take up her new role at the Sanger Institute and drive public health impact
10 Jan 2023
To influenza and beyond
The Sanger Institute’s new Respiratory Virus and Microbiome Initiative will lead the way in developing the genomic tools and methodology to study and track a range of viruses and understand how they interact with the respiratory microbiome and human hosts.
31 May 2022
COVID-19: update on SARS-CoV-2 genome sequencing at the Sanger Institute
Current status of coronavirus genome sequencing at the Sanger Institute
22 Apr 2022
Contamination control and walking with dinosaurs
Meet Laura Grout, a Quality Assurance Manager playing a vital role in genomic surveillance and UK Biobank projects at the Sanger Institute.
8 Mar 2022
Making your voice heard
Evolutionary genomics, creepy crawlies and being a woman in science
8 Mar 2022
Women rising in STEM
Reflections on working on genomic surveillance in the pandemic, and being a woman in science.
1 Mar 2022
Sequencing COVID variants: latest stats
Latest numbers for coronavirus genome sequencing at the Sanger Institute
24 Feb 2022
Genomic study shows that England’s travel quarantine measures were effective – up to a point
More than half of imported cases during period studied came from just three countries
22 Dec 2021
Rapid immune response in children protects them from COVID-19, genetic study finds
Discovery of importance of interferon response in preventing serious infection will underpin new diagnostics and therapeutics
22 Nov 2021
A Space for Science
"The most incredible things in research are the incidental findings, the serendipitous connections, moments when you are looking for one thing but you find another.”
15 Nov 2021
Covid Connections - Big Data in a Pandemic World
Researchers discuss COVID-19 genome data and its complexities, data sharing and security, and their careers in data science
14 Oct 2021
The inside story of England COVID pandemic described in new study
The most detailed analysis of SARS-CoV-2 genomics surveillance to date shows COVID-19 as a series of overlapping epidemics rather than a ...
10 Sep 2021
Wellcome Sanger Institute recognised as Charity Times finalist for outstanding contribution to pandemic response
Staff praised for dedication and excellence as they work to sequence coronavirus genomes, helping to shape the pandemic response
9 Aug 2021
From Mild to Mortal
An expert panel discuss some of the latest research into human genetics, immunology and COVID-19.
29 Jun 2021
Covid Connections – Variant or Villain
The second COVID connections talk brought together experts from COG-UK to discuss SARS-CoV-2 variants.
27 May 2021
Genomics in a pandemic - Shedding light on the invisible
Experts from the COVID-19 Genomics UK Consortium discuss sequencing SARS-CoV-2, variants, and viral fitness landscapes.
18 May 2021
Car manufacturing, cellular biology and COVID
Rachel Nelson, head of the Cellular Generation and Phenotyping (CGaP) facility, reflects on managing science at scale, including the lessons from industries as far apart as car manufacturing and Silicon Valley.
30 Apr 2021
Championing Team Science
Professor Muzlifah Haniffa shares her thoughts achieving large-scale science.
29 Mar 2021
Fighting Pathogens with Data and Partnerships
"Data analysis in genomics means that you can work in something that is meaningful."
25 Mar 2021
Salivary gland cells revealed as sites of COVID-19 infection
Human Cell Atlas findings point to role for saliva in SARS-CoV-2 transmission
17 Mar 2021
SARS-CoV-2 infects cells via specific viral entry factors that are more abundant in elderly, men and smokers
These findings offer a molecular explanation for the reported differences in disease severity for COVID-19 patients depending on age, gender and ...
11 Mar 2021
Genomic surveillance – the world’s binoculars focused on infectious diseases
Monitoring the microorganisms that cause COVID-19, malaria, cholera and a whole range of other diseases enables researchers to track outbreaks, spot emerging drug resistance and plan interventions.
3 Mar 2021
Genomics study identifies routes of transmission of coronavirus in care homes
Genome sequencing was combined with detailed epidemiological information to examine the impact of COVID-19 on care homes and to discover how ...
12 Feb 2021
New COVID-19 saliva testing strategy could translate into easy-to-use home device
The new testing approach would be easier to collect and simpler to process in the laboratory than the current nasal-swab process.
5 Feb 2021
Sequencing COVID: our latest stats
As the sequencing hub of COG-UK, the Sanger Institute is sequencing the genomes of coronavirus samples from across the country. Get our latest numbers.
21 Dec 2020
20 Things We Learned in 2020
This has been a year that none of us will forget in a hurry. The Institute is immensely proud of the way our staff have pulled together, and the work we have managed to achieve
19 Nov 2020
COG-UK computing effort wins collaboration award for COVID-19 work
HPCwire award recognises consortium's sequencing of tens of thousands of viral genomes
16 Nov 2020
Wellcome Sanger Institute and COG-UK receive £12.2M UK Government investment for COVID-19 real-time genomic surveillance system
Institute researchers will support the COVID-19 Genomics UK consortium's work by providing high-throughput virus genome sequencing, creating surveillance software to ...
22 Oct 2020
Sequencing COVID-19 at the Sanger Institute
This photo essay goes behind the scenes of the effort to sequence the genome of the COVID-19 virus at the Wellcome Sanger Institute.
19 Aug 2020
The race to sequence SARS-CoV-2
The Sanger Institute is built for high-throughput science – but the project to sequence coronavirus demanded more samples were handled more quickly than ever before.
27 Jul 2020
Impact of The Technician Commitment
Kelly Vere, Programme Director of the Technician Commitment, explores the progress of the scheme across the UK.
16 Jul 2020
From bacterial behaviours to COVID-19
Sushmita Sridhar has paused her work on a gastroenteritis-causing bacterium to help diagnose the virus that causes COVID-19.
13 Jul 2020
Explore COVID-19 science in action with new Human Cell Atlas animation
Mapping COVID-19: How the Human Cell Atlas enhances our understanding of the disease
1 Jun 2020
From cancer, stem cells and organoids to COVID-19
Sanger scientists speak about their new roles in sequencing SARS-CoV-2 genomes.
22 May 2020
Analysis of COVID-19 Genomes reveals large numbers of introductions to the UK in March
The data reports, published by the COVID-19 Genomics UK Consortium (COG-UK), show the value in mapping COVID-19 lineages across the UK ...
7 May 2020
Sanger scientist receives Chan Zuckerberg Initiative support for COVID-19 study
Roser Vento-Tormo will use single-cell technologies to understand human immune response to SARS-CoV-2 infection and the progression of the disease
23 Apr 2020
Key nose cells identified as likely COVID-19 entry points
Study with Human Cell Atlas could help understand transmission of the virus
21 Apr 2020
Tackling COVID-19 at the Sanger Institute
Staff at the Sanger Institute have joined the fight against the global COVID-19 pandemic.
8 Apr 2020
Mapping the Human Cell Atlas - charting the body’s cellular world
The Human Cell Atlas is being used to guide future research into human development, biology, health, and disease.