Genomic Surveillance Unit

The goal of the Genomic Surveillance Unit (GSU) is to support partners around the world to achieve their vision for genomic surveillance as a practical tool for local infectious disease control and pandemic preparedness.

Why genomic surveillance?

One of the biggest challenges in the battle against infectious disease is that pathogens are continually evolving. Genomic surveillance involves sequencing the genetic material of pathogenic microbes and their vectors so that evolutionary changes that affect transmission, disease severity and susceptibility to treatment can be observed. This makes it possible to monitor the ever-changing landscape of pathogen populations in order to develop effective strategies for disease control and elimination.

What does the Genomic Surveillance Unit do?

Wellcome Sanger Institute

Sequencing at the Sanger Institute

Making genomics more accessible and easier to scale will be vital for genomic surveillance to be used as a practical tool for local infectious disease control. As such, at the Genomic Surveillance Unit we develop, run, support and maintain open products that enable the genomic surveillance needs of our partners to be met. Our products provide support all the way from sample collection in the field, through high-throughput laboratory sequencing, to the delivery and interrogation of analysis-ready data.

We work closely with our partners to identify and develop new concepts, prototypes and opportunities tailored to their specific needs. We also provide guidance and training to support partners in establishing sustainable surveillance programmes. Coupling the delivery of actionable information with support for operational research and professional development enables our partners to focus on answering their pressing public health questions.

How does the Genomic Surveillance Unit achieve this?

We collaborate with leaders of clinical, epidemiological or immunological research projects and public health agencies in endemic countries, as well as international public health bodies and funders, with a focus on:

• Strengthening capacity
  Building on successful partnerships and data-sharing networks to improve the accessibility and analysis of genomic data.

• Integrated, open data
  Producing and enabling standardised, openly available, analysis-ready data resources that are actionable for public health.

• Developing tools and methods
  Strengthening the links between discovery research, operational research and large-scale genomic surveillance to translate findings into open, easy-to-use methods and tools – with the goal of making genomics more accessible and easier to scale.

• Collaborative analysis
  Working with partners to produce timely and actionable information to guide public health interventions.

How does the Genomic Surveillance Unit operate?

Kiran Garimella

Navrongo Health Centre

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, on local infrastructure and existing knowledge and expertise. We work with partners worldwide, seeking to learn the lessons in each setting that can enable us to deliver services and products that are low-cost and easy to implement in others.

As an experienced implementation partner, the Unit can help to ensure that surveillance programmes are built and used in settings that wouldn’t otherwise be possible. We know that this relies heavily on the leadership and expertise of those who are deeply familiar with the local setting. We therefore work with our partners’ local leaders, particularly in low- and middle-income countries, to try and help them identify sources for long-term, in-country funding for their genomic surveillance needs.

By collaborating closely with partners under a range of different models, the Genomic Surveillance Unit can provide support with design and deployment of in-country services, set up and run an outsourced end-to-end genomic surveillance service, either as a short-term or long-term solution, or develop hybrid approaches.

Under the leadership of its Director, John Sillitoe, the Unit operates through four mutually beneficial and reinforcing pillars:

• Collaboration
  Support global partners in various ways, ranging from providing advice and support for design and deployment of in-country services through to outsourced service delivery.

• Service
  Operate part or all of a genomic surveillance system on behalf of countries or institutions.

• Training
  Offer long-term secondment and genomic surveillance training programmes to partners.

• Product development
  Develop openly available tools and methods that strengthen the capability for establishing in-country surveillance programmes and that produce genomic data of practical value to addressing public health questions.

Building on expertise

Dan Ross/Wellcome Sanger Institute

COVID-19 surveillance sample preparation

The Genomic Surveillance Unit is a logical progression for the Sanger Institute, providing a translational engine with which to build on the infectious disease research and surveillance already underway at the Institute and our partners around the world.

Through our extensive work with the MalariaGEN network, COVID-19 surveillance, and through the Sanger Institute’s Parasites and Microbes (PaM) Programme more broadly, we have developed deep experience in building long-term, equitable and ethical partnerships and data sharing networks with which to help partners to implement systems for genomic surveillance.

We retain intimate collaborative ties with groups across the Parasites and Microbes Programme. However, by distinguishing the infectious disease and insect vector research activity undertaken in the Parasites and Microbes Programme from our focus on the delivery of large-scale genomic surveillance, we are better able to focus on the specific public health needs of our partners.

Through our work to develop new tools and methods, we support our collaborators in Parasites and Microbes and across our partners organisations to develop the outputs of their research into products that can be deployed to strengthen their genomic surveillance programmes.

Focus areas and capabilities

We are highly collaborative and employ a multidisciplinary approach, with a blend of experience ranging from commercial engineering and product development through to in-country capacity development and scientific leadership. We are passionate about integrating scientific and operational aspects of genomic surveillance.

The Unit currently has the following key focusses and capabilities:

Public Health

• Malaria Vector Surveillance
• Malaria Parasite Surveillance
• COVID-19 Surveillance

Capabilities

• Engineering business and data systems
• Undertaking large-scale surveillance operations
• Implementing surveillance projects
• Producing analysis-ready data
• Analysis and interpretation of genome data
• Supporting and engaging partner networks

Genomic Surveillance Unit Partners

As part of our partnership with the UK Health Security Agency, we are responsible for designing and running the end-to-end delivery pipeline of the UK national facility for COVID-19 genomic sequencing at the Wellcome Sanger Institute, that brings in samples from testing labs around the country and combines multiple data streams to monitor SARS-CoV-2 variants in near real time.

We work with key partners in the Parasites and Microbes Programme and in-country, alongside the Pan American Health Organisation, to support public health laboratories across Latin America to analyse locally-generated SARS-CoV-2 sequencing data.

We also work with MalariaGEN, housing a resource centre which supports the network’s global genomic surveillance of malaria parasites and mosquitoes. Founded on the principles of equitable data sharing and local capacity building, MalariaGEN brings together hundreds of partners in over 40 malaria endemic countries.