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

Article Article scientifique Article Swiss community-based surveillance of respiratory virus co-occurrence in 2022–2024 eng 2026-03-30 author Perez Rodriguez Francisco Javier 0000-0003-0380-9625 Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Swiss National Reference Centre for Emerging Viral Infections, Geneva University Hospitals, Geneva, Switzerland. 868142 author Goncalves Cabecinhas Ana Rita Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Swiss National Reference Centre for Influenza, Geneva University Hospitals, Geneva, Switzerland. 843761 author Suter Boquete Patricia Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Swiss National Reference Centre for Influenza, Geneva University Hospitals, Geneva, Switzerland. 649426 author Spedaliero Tania Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals, Geneva, Switzerland.,Swiss National Reference Centre for Influenza, Geneva University Hospitals, Geneva, Switzerland. 816095 author Hulo Nicolas Service for Biomathematical and Biostatistical Analyses, University of Geneva, Institute of Genetics and Genomics, Geneva, Switzerland. 29577 Administration de la section de biologie (BIAD) author Kaiser Laurent 0000-0002-0857-2252 Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland. 28229 Département de médecine (DEMED) author Eckerle Isabella Anne 0000-0002-4850-7172 Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland. 894639 Département de médecine (DEMED) author Essaidi-Laziosi Manel 0000-0003-1643-4965 Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals and University of Geneva, Geneva, Switzerland.,Division of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.,Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland. 682799 Département de médecine (DEMED) e03088-25 10.1128/spectrum.03088-25 41910144 2165-0497 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. Co-detection Co-occurrence Interference Respiratory viruses Virus-virus interaction and surveillance Dewey 616 Dewey 590 HUG Private Foundation ME11710 54 Département de microbiologie et médecine moléculaire 21B 56 Département de médecine 221 23 Institut de génétique et de génomique 0DH false 400 Virologie clinique 668 1255 Virus émergents 993 Microbiology spectrum fdf83246-62eb-4012-9153-fa604dbf6622 Article (Published version) Public pérez-rodríguez-et-al-2026-swiss-co.pdf 2759811 application/pdf CC BY-4.0 b70a1e0f8ec727c5c2c64d26db2c9a683582d2ba6305dc1b383197640141f3c7 6709ce3e-fae5-4c17-a2f1-8e06b09f0b84 Supplemental data Public spectrum.03088-25-s0001.docx 1047104 application/vnd.openxmlformats-officedocument.wordprocessingml.document 0237089803602676d79010c225e174b9cf16218b9460e56bbfcda1049c85816c openAccess Faculté de médecine / Section de médecine fondamentale / Département de microbiologie et médecine moléculaire Faculté de médecine / Section de médecine clinique / Département de médecine Centres et instituts / Institut de génétique et de génomique

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Swiss community-based surveillance of respiratory virus co-occurrence in 2022–2024	Microbiology spectrum			2026	8	5

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Spedaliero, Tania