Changes in respiratory viruses in infancy during the SARS-CoV-2 pandemic: a prospective cohort study

Background Respiratory virus infections are a major cause of morbidity in early life. During the SARS-CoV-2 pandemic, non-pharmaceutical interventions (NPIs) lead to worldwide changes in respiratory virus epidemiology. However, evidence regarding virus circulation in the outpatient setting remains largely unknown. The aim of this study is to longitudinally assess respiratory viruses in healthy infants before and during the SARS-CoV-2 pandemic in Switzerland. Methods In this prospective observational birth cohort study, we followed 34 infants throughout the first year of life before and during the SARS-CoV-2 pandemic. We analysed 648 biweekly nasal swabs for nine different respiratory viruses by Multiplex-PCR and assessed respiratory symptoms, COVID-19 infections of family members and childcare status in weekly interviews. 712 nasal swabs from 32 infants analysed before the pandemic and published previously served as control group. Results During the period with strict NPIs (pandemic I), most common respiratory viruses were not detected, with a rebound (driven by Adenovirus and Parainfluenza virus) after most NPIs were relaxed (pandemic II): prepandemic: 27%, pandemic I: 19%, pandemic II: 33%; historic: 36% of collected swabs per period, p<0.001. Human rhinovirus (HRV) prevalence persisted during NPIs presence, mainly in the form of asymptomatic HRV detection: prepandemic=24%, pandemic I=19%, pandemic II=25%, historic: 25%, p=0.3. SARS-CoV-2 detection (asymptomatic and symptomatic) was low, and only present after NPIs were relaxed: pandemic II=2.4%. No severe COVID-19 infections were reported. Discussion In our cohort, infants did not contribute largely to spread of SARS-CoV-2. The role of persisting asymptomatic HRV prevalence is still unclear, but it might help to maintain population immunity to prevent more severe infections. Our results underscore the importance of capturing asymptomatic viruses via longitudinal community-based data assessment to better understand virus transmission.