From alpha to omicron: how variants shaped sars-cov-2 school transmission
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Geneva University Hospitals Switzerland
Hopkins Bloomberg School of Public Health United States
University of Bern Grégoire Michielin Ecole Polytechnique Federale de Lausanne Switzerland
cEole Polytechnique Federale de Lausanne Switzerland
Publication date: 2023-04-26
Popul. Med. 2023;5(Supplement):A479
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.

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.

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.

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.