UKHSA launches new metagenomic surveillance for health security
Source: gov.uk (2025-01-30)

The UK launches mSCAPE, a world-first metagenomics initiative by UKHSA to enhance health security through rapid pathogen detection and surveillance.

The UK has taken a leap forward in its efforts to use pathogen genomics to improve health security. Today the UK Health Security Agency (UKHSA) launches a world-first metagenomics initiative to aid in the rapid detection of infectious diseases that could threaten the UK. The metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE), which has been in development over the last year, is piloting the use of metagenomic data for public health surveillance and pathogen analysis.

The programme is a collaborative initiative, led by UKHSA and involving a consortium of NHS and academic partners including the University of Birmingham, University of Edinburgh, and the NHS Clinical Respiratory Metagenomics Network led by Guy’s and St Thomas’ NHS Foundation Trust.

UKHSA will take anonymous pathogen data from multiple labs that are using metagenomics for diagnosis, including those in the NHS, and analyse it at a national level to monitor trends, epidemiology and pathogen emergence at speed. This will allow for assessment of the ability to significantly improve identification of new outbreaks as well as enabling the source of an outbreak to be better understood, predictions to be made about the effectiveness of potential treatments, and any concerning mutations can be identified.

Effective use of metagenomic data will add a new, crucial insight to current health protection surveillance systems in the UK. mSCAPE aims to develop the capability to use this data as part of UKHSA’s ongoing surveillance of new and emerging infections, pathogens of pandemic potential, and to monitor the evolution of pathogens that cause disease.

Metagenomic methodology allows for untargeted sequencing of patient samples for the presence of pathogenic viruses and bacteria, which is a significant step forward in detection and diagnosis abilities. Traditional genomic methodologies have required scientists to target sample sequencing towards pathogens that are already known to the scientific and medical community. Pathogen-agnostic metagenomic methods do not require scientists to know for sure what pathogens are present in a sample before the sequencing is conducted.

This is a major advantage in the detection of known but unexpected pathogens for which specific tests are not readily available and for pathogens not normally found in humans. It is also beneficial in the event of the emergence of a previously unknown novel pathogen. Metagenomic sequencing is becoming established as a clinical diagnostic test, and its use is currently being expanded in the NHS (https://www.gov.uk/government/news/uk-to-create-world-first-early-warning-system-for-pandemics).

Professor Susan Hopkins, UKHSA Chief Medical Advisor, said:

Genomics has been a crucial aspect of the response to the COVID-19 pandemic from the very start, and the UK’s enormous technical expertise in this area has allowed us to play a leading role in the identification and analysis of COVID-19 variants as they emerge.

The new mSCAPE programme will allow us to use the UK’s leading genomics capability to conduct community surveillance using pathogen-agnostic sequencing data for the first time anywhere in the world, and our new initiative to share our pathogen genomic data demonstrates our commitment to our data being used to improve health globally.

This is a hugely exciting development which will increase our ability to respond at speed to new and emerging pathogens and will help to ensure that we are as prepared as possible to act quickly and effectively to protect the public from future threats.

Professor Dame Sue Hill, Chief Scientific Officer for NHS England and Senior Responsible Officer for NHS Genomics, said:

Genomics is revolutionising the way we predict, prevent, diagnose and treat illness – whether it’s diagnosing rare conditions in children more quickly, helping personalise cancer treatments to make them more effective, or identifying people at greater risk from kidney disease.

The mSCAPE programme is another great example of how the UK is leading the world in this field, and we are pleased to be able to support it through our Networks of Excellence in Severe Respiratory Infections.