Swiss community-based surveillance of respiratory virus co-occurrence in 2022–2024

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Viral respiratory infections (VRIs) are a persistent global health concern, driven by the year-round circulation of diverse viruses. During the coronavirus disease 2019 (COVID-19) pandemic, the prevalence of most respiratory viruses declined sharply following nonpharmaceutical interventions. Their subsequent resurgence and co-circulation with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) created a novel and unpredictable VRI landscape. We investigated the respiratory virus dynamics and co-occurrence patterns in symptomatic outpatients in Switzerland, using nasopharyngeal specimens collected between August 2022 and July 2024 by the National Reference Center for Influenza. In total, 5,369 specimens were tested by PCR or RT-PCR for 16 respiratory viruses. Co-detections were identified in 9% of positive samples and occurred year-round. The majority involved two viruses (92%), although triple and quadruple detections were also observed. Statistical analysis showed that multiple detections were significantly more common in children. Their incidence was higher not only with the most prevalent ones, rhinoviruses (RVs) and SARS-CoV-2, but also with bocaviruses (hBoV) and adenoviruses (ADVs). A statistically significant decrease in viral load was observed when a second virus was co-detected with SARS-CoV-2 or respiratory syncytial virus (RSV), but not with influenza viruses. This effect was most pronounced in early- and middle-aged adults. Through the systematic investigation of viral co-occurrence, this study emphasizes the importance of community-based surveillance. Beyond monitoring respiratory disease burden, such surveillance provides a foundation for generating hypotheses to better understand viral interactions and the virus-host interplay during infection.IMPORTANCEViral respiratory infections (VRIs) are a major public health challenge due to their constant circulation and significant impact on vulnerable populations. The coronavirus disease 2019 (COVID-19) pandemic profoundly altered the dynamics of respiratory viruses, leading first to a sharp decline in their prevalence, followed by an unpredictable resurgence in co-circulation with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). In this context, understanding viral interactions and their co-detection in the community has become essential. This project provides novel insights into the frequency and characteristics of viral co-infections in a real-world outpatient setting. It highlights age-related differences and demonstrates statistically significant effects on viral load, particularly for SARS-CoV-2 and respiratory syncytial virus (RSV). These findings underscore the importance of community-based surveillance, not only to monitor the overall burden of respiratory diseases but also to generate new hypotheses on virus-host interactions. Ultimately, this knowledge can guide the development of more effective prevention and management strategies.

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