BACKGROUND: In 2018, a hospital-based surveillance system for influenza (CH-SUR) was established in six tertiary care hospitals in Switzerland. From March 2020 onwards, this surveillance system was expanded to include more institutions, as well as COVID-19.

AIM: To quantitatively evaluate the timeliness and completeness of CH-SUR data and to qualitatively assess stakeholder perceptions of the importance, reliability and adaptability of the surveillance system.

METHODS: All patients admitted to one of the participating centres for more than 24 hours and who had a laboratory-confirmed influenza virus or SARS-CoV-2 infection were included in CH-SUR. For all cases, we evaluated the timeliness and completeness of reporting to CH-SUR. A qualitative survey among CH-SUR stakeholders assessed perceived importance, understanding, reliability and adaptability of CH-SUR.

RESULTS: Up to 20 centres participated in CH-SUR. Between December 2018 and October 2023, 7375 cases of influenza were reported and between March 2020 and October 2023, 49,235 cases of COVID-19 were reported to CH-SUR. During the COVID-19 pandemic, time to data entry and completeness improved over time; the median delay of data entry in CH-SUR was 5 days (interquartile range [IQR]: 2–23) for COVID-19 and 4 days (IQR: 2–15) for influenza during the period 2018–2023. The completeness of variables was high (99.4%), with the exception of COVID-19 or annual influenza vaccination status (respectively, 15% and 72% “Unknown” responses). Stakeholders perceived the system as important, relevant, understandable and adaptable.

CONCLUSION: CH-SUR provided critical epidemiological and clinical information on hospitalised influenza and COVID-19 cases across Switzerland during the pandemic. Our evaluation highlighted the importance and relevance of this system among CH-SUR stakeholders, as well as its importance for preparedness and response to future infectious disease outbreaks.