Utility of SARS-CoV-2 Genomic Sequencing for Understanding Transmission and School Outbreaks

Abstract

Objective: An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period.

Study design: School outbreaks were identified for sequencing by local public health units based on multiple cases without known epidemiological links. Cases of SARS-CoV-2 from students and staff from 4 school outbreaks in Ontario underwent WGS and phylogenetic analysis. The epidemiological clinical cohort data and genomic cluster data are described to help further characterize these outbreaks.

Results: A total of 132 positive SARS-CoV-2 cases among students and staff from 4 school outbreaks were identified with 65 (49%) of cases able to be sequenced with high-quality genomic data. The 4 school outbreaks consisted of 53, 37, 21 and 21 positive cases; within each outbreak there were between 8 and 28 different clinical cohorts identified. Among the sequenced cases, between 3 and 7 genetic clusters, defined as different strains, were identified in each outbreak. We found genetically different viruses within several clinical cohorts.

Conclusions: WGS, together with public health investigation, is a useful tool to investigate SARS-CoV-2 transmission within schools. Its early use has the potential to better understand when transmission may have occurred, can aid in evaluating how well mitigation interventions are working and has the potential to reduce unnecessary school closures when multiple genetic clusters are identified.

FIGURE 1.

Epidemic curves. Molecular-confirmed cases of SARS-CoV-2 are shown for each school outbreak (A–D). Complete genomic data indicates a genome coverage ≥90%, while incomplete/no genomic data indicates that either <90% coverage, or the specimen was unavailable for genomic testing.

FIGURE 2.

Phylogenetic trees. Phylogenetic analysis of 4 school SARS-CoV-2 outbreaks (A–D). Staff cases are indicated in all upper-case letters, while student cases are in lowercase letters. Individuals that were symptomatic at the time of collection have open circles, and cases asymptomatic at the time of collection have closed circles. All trees are rooted to the reference genome MN908947.3 with the scale representing nucleotide substitutions per site based on the full viral genome.