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

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.