Background: Since the emergence of COVID-19, countries have implemented combinations of non-pharmaceutical measures not only to contain the COVID-19 cases manageable for their healthcare system but also to reduce the economic burden of the disease. Among the various options, authorities have mostly adopted frequent hand disinfection and wearing surgical masks. Because these measures have long been used in medicine to prevent infections, there is reason to expect an effect not only on SARS-CoV-2 but also on other microorganisms that spread via droplet inhalation and close contact. This study investigates the epidemiology of typical respiratory viruses in Slovenian hospitalized patients before and during the ongoing SARS-CoV-2 epidemic.

Methods: Molecular testing data were analyzed using a laboratory informative system for typical respiratory viruses from 2012 to 2022 in conjunction with SARS-CoV-2 testing from March 2020 onward.

Results: First, we observed a significant decrease in the number of typical respiratory virus testing requirements after the SARS-CoV-2 outbreak; second, a change in the age structure of hospitalized patients, with fewer children and more working-age individuals during the 2020/21 season; third, complete disappearance of influenza A, B, RSV, and other enveloped respiratory viruses; and, fourth, unchanged epidemiology of rhinovirus. Finally, with the slow fading of all measures implemented in the 2020/21 season, respiratory viruses appear to be “back on the scene” despite the still ongoing SARS-CoV-2 epidemic in 2021/22.

Conclusions: Further monitoring seems to be important in the coming seasons to shed more light on future changes in respiratory viruses’ epidemiology because restrictions are bound to be loosened.