Genomic Surveillance Unit
Why genomic surveillance?
One of the biggest challenges in the battle against infectious disease is that pathogens are continually changing. They can evolve to escape immune systems, vaccines, drugs, and most interventions humans can devise.
By sequencing the genetic material of both the pathogens that cause disease and their animal vectors, we can track mutations that affect transmission, disease severity, and susceptibility to treatment. This makes it possible to monitor the constantly shifting landscape of pathogen and vector populations and develop strategies that work both today and in the future.
What does the Genomic Surveillance Unit do?
The GSU brings expertise in genomics, data science, product development, and sequencing operations to bear on surveillance solutions for important human diseases. We currently focus on malaria, COVID-19, and a range of other respiratory viruses.
Our world-leading COVID-19 and malaria genomic surveillance streams have a proven track record of successful implementation. We support partners around the world at every stage of the process, from sample collection and lab setup to training, data generation, and analysis.
The GSU is led by John Sillitoe, and our priorities are to continually increase benefits to public health, while improving the accessibility and quality of genomic surveillance data. We seek to maximise the volume, quality, and scale of information that can be obtained from a sample and work to reduce the time to stand up functioning surveillance solutions. Driven by the needs of our partners, we create analytical tools, lab methods, and data pipelines that push the boundaries of what’s possible.
Current surveillance activities
Malaria Parasite
The Plasmodium parasites that cause malaria have a remarkable ability to survive. Through small genetic changes, they can evade the human immune system, develop resistance to antimalarial drugs, and adapt to changes in the Anopheles mosquitoes that transmit the parasites. Cristina Ariani leads the team in the Genomic Surveillance Unit responsible for building data products and creating new scientific techniques that help track these genetic changes.
Learn more about Malaria Parasite Genomic Surveillance
Malaria Vector
Malaria vector control, particularly in Africa, is going through a period of major change. New insecticides are being brought into use through a new generation of long-lasting insecticide-treated nets (LLINs) and indoor residual spraying (IRS) products. These new tools are currently effective, but we know from past experience that mosquitoes will evolve resistance. Without preemptive action, these tools will not remain effective for long. Alistair Miles leads the team in the Genomic Surveillance Unit that builds data products to track the evolution of insecticide resistance in Anopheles mosquitoes in Africa and Southeast Asia.
Learn more about Malaria Vector Genomic Surveillance.
COVID-19
When COVID-19 hit and millions of samples of a previously unknown virus were collected by labs across the UK, the deep expertise at the Wellcome Sanger Institute for large-scale sequencing, analysis, and discovery became a crucial resource. At the peak of the pandemic, the COVID-19 team at Sanger were sequencing 70,000 samples per week to discover new variants.
While the volume has since decreased, it remains crucial to track variants of the SARS-CoV-2 virus that have potential to cause further harm. Sonia Goncalves leads the team in the Genomic Surveillance Unit responsible for delivering high-quality SARS-CoV-2 data to the UK Government and to the public.
As part of our partnership with the UK Health Security Agency (UKHSA), we are responsible for designing and running the end-to-end delivery pipeline of the UK’s national facility for SARS-CoV-2 genomic sequencing at the Wellcome Sanger Institute. We bring in samples from testing labs around the country and combine multiple data streams to monitor SARS-CoV-2 variants in near real time.
Future surveillance activities
Respiratory Viruses
Millions of diagnostic swabs were sent to the Sanger Institute for sequencing during the COVID-19 pandemic. These swabs also contain DNA for all the other microbes that were present in patients’ respiratory tracts at the time.
A team in the Wellcome Sanger Institute’s Parasites & Microbes programme led by Ewan Harrison is developing the techniques required to turn the genetic material on these swabs into a map of the respiratory microbiome of Britons over the past two years. Once the technique is developed, the Genomic Surveillance Unit will scale up the products that will enable public health partners to track, in near-real-time, exactly which variants of flu, respiratory syncytial virus, and SARS-CoV-2 are circulating.
How we work
Establishing integrated end-to-end genomic surveillance systems is a complex process. Requirements vary widely depending on the nature of the infectious disease agent or vector organism. They also depend on local infrastructure and existing knowledge and expertise. We work with partners worldwide, seeking to learn the lessons in each setting that can help us to deliver services and products that are low-cost and easy to implement.
Underpinning the surveillance streams are the following capabilities, each represented by a team within the Genomic Surveillance Unit:
- Creating efficient business systems and digital products (Digital Systems & Infrastructure)
- Ensuring surveillance operations run smoothly and effectively (Surveillance Operations)
- Managing a variety of specialised genomics projects (Implementation Management)
- Curating data to make it ready for further analysis (Data analysis and engineering)
- Supporting and engaging partner networks (Partnerships, Engagement & Growth)