Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data

Abstract

Mathematical modelling studies have shown that repetitive screening can be used to mitigate SARS-CoV-2 transmission in primary schools while keeping schools open. However, not much is known about how transmission progresses within schools and whether there is a risk of importation to households. During the academic year 2020-2021, a prospective surveillance study using repetitive screening was conducted in a primary school and associated households in Liège (Belgium). SARS-CoV-2 screening was performed via throat washing either once or twice a week. We used genomic and epidemiological data to reconstruct the observed school outbreaks using two different models. The outbreaker2 model combines information on the generation time and contact patterns with a model of sequence evolution. For comparison we also used SCOTTI, a phylogenetic model based on the structured coalescent. In addition, we performed a simulation study to investigate how the accuracy of estimated positivity rates in a school depends on the proportion of a school that is sampled in a repetitive screening strategy. We found no difference in SARS-CoV-2 positivity between children and adults and children were not more often asymptomatic compared to adults. Both models for outbreak reconstruction revealed that transmission occurred mainly within the school environment. Uncertainty in outbreak reconstruction was lowest when including genomic as well as epidemiological data. We found that observed weekly positivity rates are a good approximation to the true weekly positivity rate, especially in children, even when only 25% of the school population is sampled. These results indicate that, in addition to reducing infections as shown in modelling studies, repetitive screening in school settings can lead to a better understanding of the extent of transmission in schools during a pandemic and importation risk at the community level.

Keywords: Outbreak reconstruction; Primary school; SARS-coV-2 transmission; Screening protocol; Whole genome sequences.

Fig. 1

Compliance to the study protocol over time by participant group. Compliance is defined as the number of samples obtained divided by the expected number of samples for each week. Dotted vertical lines indicate weeks of school holidays when no samples were collected.

Fig. 2

Time-scaled maximum likelihood tree. The tree is rooted on the reference sequence (ref) which represents an isolate obtained early in the pandemic. Branches are coloured according to pangolin lineage.

Fig. 3

Consensus transmission tree under the baseline scenario from the Outbreaker2 model. The consensus tree is defined as the tree with the modal posterior ancestor for each case. Indirect transmission (dashed line) means at least one unobserved intermediate case is present.

Fig. 4

Uncertainty in ancestry assignment for the different models. For each case, uncertainty is quantified as the Shannon entropy of the posterior distribution of potential infectors. Only 36 cases are included in the SCOTTI model. Higher values indicate a larger number of plausible infectors, hence higher uncertainty in ancestry assignment.

Fig. 5

Accuracy of estimated weekly positivity rates. Accuracy is defined as the absolute deviation (observed minus true positivity rate) in estimates of the weekly positivity rate (in %) for different proportions of the school sampled. Black crosses represent the median deviation among 100 simulated outbreaks. In the baseline scenario, testing was performed once a week.