Extending influenza surveillance to detect non-influenza respiratory viruses of public health relevance: analysis of surveillance data, 2015-2019, Belgium

BACKGROUND: Seasonal influenza-like illness (ILI) affects millions of people yearly. Severe acute respiratory infections (SARI), mainly caused by influenza, are a leading cause of hospitalisation and mortality. Increasing evidence indicates that non-influenza respiratory viruses (NIRVs) also contribute to the burden of SARI. In Belgium, SARI surveillance by a network of sentinel hospitals is ongoing since 2011. AIM: Here, we report the results of using in-house multiplex PCRs for the detection of a flexible panel of viruses in respiratory ILI and SARI samples and the estimated incidence rates of SARI associated to each virus. METHODS: ILI was defined as an infection with onset of fever and cough or dyspnoea. SARI was defined as an infection requiring hospitalization with onset of fever and cough or dyspnoea within the previous 10 days. Samples were collected during four winter seasons and tested by multiplex RT-qPCRs for influenza virus and NIRVs. Using catchment population estimates, incidence rates of SARI associated to each virus were calculated. RESULTS: One third of the SARI cases were positive for NIRVs, reaching 49.4% among children under fifteen. In children under five, incidence rates of NIRV-associated SARI were double that of influenza (103.4 versus 57.6 per 100000 person-months), with NIRV co-infections, respiratory syncytial viruses, human metapneumoviruses and picornaviruses contributing the most (33.1, 13.6, 15.8 and 18.2 per 100000 person-months, respectively). CONCLUSION: Early testing for NIRVs could be beneficial to clinical management of SARI patients, especially in children under five, for whom the burden of NIRV-associated disease exceeds that of influenza.