Metagenomic sequencing methods can target multiple pathogens within a single sequencing workflow, expanding the range of pathogens targeted routinely and providing the potential to spot novel or rare pathogens as part of pandemic preparedness. To evaluate the potential of routine metagenomics in respiratory virus surveillance, we sequenced from the SARS-CoV-2 Immunity and Reinfection Evaluation (SIREN) study of healthcare workers throughout the United Kingdom. During winter 2023-2024, participants submitted nasopharyngeal swabs and symptom questionnaires fortnightly. Swabs were tested for SARS-CoV-2, Influenza (A and B), and RSV via qPCR, and residual nucleic acid from swabs underwent targeted metagenomic sequencing. All Influenza and RSV qPCR positive samples were submitted for sequencing and a subset of qPCR negative samples were selected for sequencing based on their symptoms.  In total, 720 qPCR positive and 3,584 qPCR negative samples were sequenced. We identified multiple co-infections in the Influenza and RSV samples and detected rhinoviruses, seasonal coronaviruses, metapneumovirus, parainfluenza viruses, and adenoviruses in qPCR negative samples. Importantly, we detected viruses before the onset, and in the absence, of respiratory symptoms in a sizable number of samples. Metagenomic sequencing provided insights into the genomic epidemiology and dynamics of Influenza, RSV and other respiratory viruses across the country and throughout winter. This work demonstrates the utility of high-throughput multi-virus sequencing for surveillance and has important public health implications to develop interventions to mitigate the winter pressures experienced by healthcare systems.