Background and objective:
SARS-CoV-2 transmission among young children in schools is of major importance due to their potential role in fueling community-wide transmission. Initial studies found little within-school transmission, with few reports after more infectious variants emerged. We aimed to determine how variants of concern (VOCs) altered within-school transmission dynamics among young children.

Methods:
We implemented a prospective observational surveillance study in 3 pre-school and 2 primary schools in the canton of Geneva, Switzerland. We sampled children between 2 and 6 years of age, educational staff, and household members. We collected oral-swab PCR tests, capillary blood for anti-spike serology and questionnaires for household and class members at the time of outbreak declaration and at two subsequent time points (day+2 and day+30). All available virological samples underwent whole genome sequencing. We developed a mathematical model of SARS-CoV-2 transmission to infer time-varying force of infection within schools and from the community at large.

Results:
Between March 2021 and June 2022, we recruited a total of 351 children and 107 staff, and 111 of their household members. We investigated eleven SARS-CoV-2 outbreaks (two Alpha, six Delta and three Omicron), involving a total of 33 classes. Phylogenetic analysis on 56 available sequences from seven of the outbreaks (one Alpha, three Delta and three Omicron) indicate that clustering differed between variants, with a higher degree within-school clustering for the Alpha outbreak and lower for the Omicron outbreaks. Modeling results integrating epidemiological and genetic data supported a changing importance of within-school vs. community transmission as more infectious variants emerged.

Conclusion:
The importance of within-school SARS-CoV-2 transmission changed with the emergence of more infectious variants. The potential impact of interventions in educational settings depends on these changes and could be tailored to specific transmission scenarios.