Background

Childhood mortality due to SARS-CoV-2 remains low until now. However, consequences of asymptomatic carriage or pandemic control measures are unclear. Respiratory viral infections are a major cause of morbidity in children. It is thus important to understand how SARS-CoV-2 infections or prevention measures affect the transmission of common respiratory viruses.

Objectives

We aimed to study the prevalence of SARS-Cov-2 and common respiratory viruses in healthy infants before and during the pandemic.

Methods

Biweekly nasal swabs of 34 healthy infants from a Swiss birth cohort study followed throughout the first year of life were analysed for 9 different viruses by multiplex-PCR. Respiratory symptoms were assessed by weekly telephone interviews. We compared data assessed prior the pandemic (E1, n=94), during strict lockdown measures (E2, n=215), and when most restrictions were relaxed (E3, n=339).

Results

We analysed 648 nasal swabs from 2019-2022. In 179 (28%) of all swabs we found any respiratory virus and of those 40 (23%) were symptomatic. Virus prevalence overall was lower during first lockdown compared to data assessed before, followed by a rebound of respiratory viruses after restrictions were relaxed (27% E1, 19% E2, 33% E3; p=0.001). Rhinovirus persisted during the study period, whereas e.g. Adenovirus vanished in E2 with a strong increase in E3. SARS-CoV-2 was only detected in E3 and prevalence was low (2.4%) with only 25% being symptomatic.

Conclusion

SARS-CoV-2 infections as well as asymptomatic carriage in our cohort are low. However, we saw relevant alterations of viral colonization driven by measures of precaution with still unknown epidemiological consequences.