Viral metagenomic sentinel surveillance of acute respiratory infections in primary care as a public health strategy: a prospective national pilot study

ABSTRACT

Summary Background With the introduction of metagenomics in clinical diagnostics unfolding and the expanding role of pathogen genomics in national surveillance, the stage is set for its launch into public health surveillance. This report pilots the use of metagenomics for nationwide sentinel general practitioner (GP) monitoring and genomic characterisation of both anticipated and emerging respiratory viruses in primary care. Methods This prospective pilot study included a selection of 93 patients with acute respiratory illness in GP practices participating in nationwide sentinel virological surveillance during winter 2024-2025. Specimens underwent parallel metagenomic testing using probes targeting human and animal viruses. The primary outcome was detection and in-depth genomic characterisation of viruses covered by standard screening and those outside the scope of standard methods. Findings Metagenomic surveillance detected viruses in 95% of the specimens, including latent ones. Overall, 83% of specimens were positive by standard PCR-based screening. For viruses targeted by routine PCR, metagenomics showed a sensitivity of 94% (95%CI 86-97), specificity of 100% (95%CI 99-100), positive predictive value of 96% (95%CI 89-99), and negative predictive value of 100% (95%CI 99-100), with median genome coverage of more than 99% (95%CI 23-100%). Metagenomic data enabled instant full genomic characterisation of circulating viruses targeted by current amplicon-based surveillance, including influenza viruses, SARS-CoV-2, and respiratory syncytial viruses (RSV), as well as less frequently targeted viruses such as human metapneumoviruses (hMPV), betacoronaviruses OC43 and HKU1, and non-targeted viruses such as adenoviruses. The data facilitated characterisation of a reassortant H3N2 influenza virus, potential vaccine escape mutants, markers of susceptibility to influenza antiviral drugs and RSV monoclonal antibodies, and a human H1N2 swine influenza virus infection, demonstrating comprehensive and robust performance regardless of the circulating viruses. Interpretation In this pilot study, metagenomic data enhanced standard typing through its broad scope and simultaneous detection and genome characterisation, enabling drug and vaccine resistance monitoring. These capabilities support the potential of metagenomics to expand current diagnostic approaches and gradual integration into public health surveillance. Funding The Netherlands Organisation for Health Research and Development (ZonMw), and Ministry of Health, Welfare and Sport (VWS). Research in context Evidence before this study To identify studies using metagenomics for screening of patients with infectious diseases, we searched PubMed using the following search terms in the title/abstract: (metagenomic OR metagenomics OR mNGS) AND (prospective OR trial OR RCT). The results were filtered for prospective studies involving humans and written in English. The search was performed on December 10, 2025. The search results showed an exponential growth of prospective clinical studies on metagenomics, from only a few publications in 2021 to over 90 reports up to end-2025. The typical setting was diagnostic testing in hospitalised patients, and the primary focus of clinical performance assessment was detection as a dichotomous outcome rather than full genome characterisation. Around 80% of all prospective studies were observational: while sampling was prospective, metagenomic results were not reported in real-time as part of the study. One prospective study focused on respiratory metagenomic testing of outpatients in a public health setting. The study explored the use of untargeted metagenomics in Swiss outpatients, comparing COVID-19 pre-pandemic and pandemic periods, with retrospective reporting. This comparative study was limited to detection while the untargeted metagenomic approach did not demonstrate full genome characterisation. A recent News report in this journal announced the launch of the UK metagenomic Surveillance Collaboration and Analyses Programme (mSCAPE) for winter 2025-26, leveraging clinical metagenomic data from diagnostic laboratories in hospitalised patients for surveillance purposes. To our knowledge, no pilot results from this initiative have been reported to date. Added value of this study These data represent the first on the performance and feasibility of metagenomic surveillance integrated within the existing nationwide primary care sentinel GP infrastructure for genomic virological surveillance of acute respiratory infections. By performing viral detection and providing simultaneous full genome consensus sequences, typing of all circulating respiratory pathogens, as well as antiviral reduced susceptibility and antibody escape mutation analyses, could be performed directly. Prospective inclusion and metagenomic analyses were conducted in parallel with standard analyses and reporting to GPs and national and international stake holders. Although the metagenomic data delayed virus detection reporting compared to the standard approach, it outperformed standard surveillance sequencing by enabling full genome characterisation of all circulating viral pathogens, highlighting its potential in sentinel GP surveillance of acute respiratory infections. Implications of all the available evidence Evidence is emerging that metagenomic approaches are effective and feasible for implementation not only in the clinical diagnostic setting but also for genomic characterisation in outpatient public health settings.