mSCAPE: a national collaboration using metagenomics to protect public health

At the London Calling conference earlier this year, we heard about the potential of metagenomic Oxford Nanopore sequencing to deliver rapid, accurate respiratory pathogen detection in a matter of hours¹. Using untargeted sequencing of microbial nucleic acids in clinical research samples, an assay developed by the NHS Clinical Respiratory Metagenomics Network, led by Guy’s and St Thomas’ NHS Foundation Trust, UK, rapidly detects bacteria, viruses, fungi, and parasites in one go. Now being developed and validated at multiple NHS sites across the UK, this pathogen-agnostic assay shows potential to considerably change the way infectious diseases are identified and managed in the future². However, the fight against infectious disease doesn’t stop there.

Now, a collaboration of researchers and public health teams is using this same metagenomic data to protect public health at a national level. In this blog, find out how Oxford Nanopore sequencing data feeds into the Metagenomics Surveillance Collaboration and Analysis Programme (mSCAPE)³ to help safeguard against the threat of future pandemics.

The first pathogen surveillance network of its kind

In 2024, a landmark partnership was announced between Oxford Nanopore Technologies, the UK Government, the UK Biobank, and NHS England⁴. Its goals include the creation of an ‘early warning system’: a first-of-its-kind real-time pathogen surveillance system to monitor for future infectious disease outbreaks. Genomic pathogen surveillance played a critical role in responding to COVID-19, allowing researchers to monitor its spread and rapidly identify significant new variants as the SARS-CoV-2 virus evolved⁵.

The partnership’s goals also include expansion of the respiratory metagenomics assay that, as well as showing clinical potential to characterise infectious diseases, would also rapidly provide data for this surveillance system.

In this pan-microbial workflow, researchers at UK NHS sites first extract DNA and RNA from respiratory clinical research samples, without any need for time-consuming culture or prior knowledge of which microbes they may contain¹. They then prepare libraries using the Rapid PCR Barcoding Kit and sequence on a GridION. Next, this data travels down two very different paths.

Clinical potential and public health safeguarding — from the same data

For the first path, the researchers use a bioinformatics pipeline that they developed in house to accurately identify the pathogens present in these mixed microbial samples in real time, with the first actionable results ready in approximately six hours — instead of the days or weeks often required using multiple legacy techniques. Beyond identification, the data also reveals antimicrobial resistance (AMR) genes and enables deep genomic characterisation, showing future potential to inform effective treatment and antimicrobial stewardship. The UK NHS Respiratory Metagenomics Network is seeking ISO 15189 clinical laboratory accreditations for this assay as it is rolled out.

The second path is where mSCAPE comes in. Launched in 2025, the programme, led by the UK Health Security Agency (UKHSA), brings together a consortium of NHS and academic institutions, including the NHS Clinical Respiratory Metagenomics Network⁶.

Anonymised metagenomic data from this source and others is uploaded via the data sharing platform mSCAPE.CLIMB, using the same core computing infrastructure as used for COVID-19 surveillance in the UK⁷. In this pilot programme, researchers and public health teams are exploring how this multidimensional data can be used to identify pathogens that could represent future pandemic risk. As of July 2026, the mSCAPE platform had processed datasets from over 6,000 clinical research samples, nearly half of which were directly from the NHS⁸.

No microbe left behind

Why use metagenomic nanopore sequencing data for this undertaking? Firstly, turnaround time is key. Presenting in a UKHSA webinar, Dr Meera Chand (UKHSA) highlighted the difficulties of keeping up with the rapid pace of outbreaks, requiring a combination of global intelligence on circulating pathogens and assessment of the risk and scale of potential UK outbreaks⁹. In contrast, Meera explained, by integrating routine, timely genomic pathogen surveillance nationally, this prior knowledge is not required. Instead, any unusual circulating pathogens can be identified, assessed for risk, and monitored — in time to enact public health measures to mitigate their spread where needed. Integrating rapid nanopore sequencing workflows directly into clinical research settings allows this fast flow of data.

Another critical element is the nature of metagenomic nanopore sequencing data itself. Long nanopore reads facilitate accurate detection of even closely related microbial strains from mixed samples, as well as AMR genes. Identification is not limited to only culturable microbes, or to panels of pre-selected microbes as used in targeted tests. Instead, this pan-microbial approach allows researchers to detect seasonal, rare, and potentially concerning pathogens that could otherwise be missed.

As well as offering clinical potential, this unbiased approach is crucial for identifying uncommon or novel microbes that could spread to the epidemic or pandemic level. Researchers using the respiratory metagenomics assay have already identified influenza C — which was previously thought to be uncommon in humans and is not tested for via PCR — and zoonotic spillovers including avian paramyxovirus and Chlamydia psittaci¹.

Presenting in the UKHSA webinar, Prof. Nicholas Loman (University of Birmingham, Public Health Genomics, UKHSA) stressed the importance of the ‘rapidly pivoting’ mSCAPE network for pandemic preparedness⁹. By connecting sequencing experts, bioinformaticians, and public health teams, the platform is already providing a live stream of metagenomic data and information on pathogens of high concern. As the pilot programme continues to develop, the team also plan to integrate environmental samples, from sources such as aircraft wastewater, to expand its range further still.

This metagenomic approach shows potential for a future in which infectious disease is tackled on three fronts: by rapid identification and treatment of infections in clinical settings, effective antimicrobial stewardship to address the threat of drug-resistant organisms, and finally, monitoring for potential outbreaks through a comprehensive, collaborative pathogen surveillance network. Combined, these efforts hold the potential to address the burden of infectious disease on a national scale.

Want to find out more?

Discover the potential of metagenomic sequencing to safeguard public health in our white paper: Delivering the future of genomic pathogen surveillance with Oxford Nanopore sequencing.

Learn about the rapid assay developed by the NHS Respiratory Metagenomics Network: Pan-microbial pathogen detection in hours using metagenomic sequencing.

Oxford Nanopore Technologies products are RUO. Products labelled/branded as OND may be RUO or may be regulated as in-vitro diagnostic devices in some jurisdictions.