Outbreak Associated With SARS-CoV-2 B.1.617.2 (Delta) Variant in an Elementary School

Marin County, California, May-June 2021

Tracy Lam-Hine, MBA; Stephen A. McCurdy, MD; Lisa Santora, MD; Lael Duncan, MD; Russell Corbett-Detig, PhD; Beatrix Kapusinszky, PhD; Matthew Willis, MD


Morbidity and Mortality Weekly Report. 2021;70(35):1214-1219. 

In This Article

Public Health Response

On May 26 and June 2, MCPH held testing events at the school as part of outbreak control. During these 2 days, 231 persons were tested, including 194 of 205 students, 21 of 24 staff members and teachers, and 16 parents and siblings of students. The California Department of Public Health assisted with guidance, application of additional prevention strategies, and on-site testing. Community contacts and all students and staff members were encouraged to participate. Specimens for WGS were collected during May 26–June 12; all 18 positive specimens with detectable virus (cycle threshold value <32) were sequenced using ClearDx instruments (Clear Laboratories), Oxford Nanopore MinION sequencing technology, and SARS-CoV-2 ARTIC V3 protocol for amplicon sequencing. Consensus genome assembly was performed in Terra using Titan Clear Laboratories workflow.§ All sequences generated were classified as the Delta variant. A phylogenetic tree was constructed using the UShER pipeline and visualized using Auspice.us [4] (Figure 3). Eleven sequences were genetically indistinguishable from one another; seven sequences contained additional single nucleotide variations. Among the indistinguishable specimens, six were from students of the index patient, four were from students in the separate grade, and one was from a sibling of a student in the index patient's class, suggesting that infections occurring in the two grades likely were part of the same outbreak. The epidemiologic link between the two grades remains unknown but is thought to be interaction at the school. Five additional related sequences from community cases (in two adults and three children) were later identified, including three more genetically indistinguishable sequences. One was from an adult with specimen collection 1 day before symptom onset in the index patient. Case investigation records did not establish an epidemiologic link between these five community cases and the school outbreak.

Figure 3.

Phylogenetic tree*,† of SARS-CoV-2 whole genome sequences and specimen collection dates§ from a COVID-19 outbreak in an elementary school — Marin County, California, May–June 2021
Abbreviations: SNV = single nucleotide variant; WGS: whole genome sequencing.
*Phylogenetic tree was created with UShER, which uses the Fitch–Sankoff algorithm (a maximum parsimony-based phylogenetic placement approach). https://www.nature.com/articles/s41588-021-00862-7
Specimen for the index patient was not available for WGS and is not included on the phylogenetic tree.
§Dates in this diagram reflect the collection date for specimens that underwent WGS; thus dates might differ from those reported in the text for persons whose initial specimens were discarded.
Branches are labeled with SNVs; cases (circles) are color-coded to indicate social relationship within the outbreak and labeled with the collection date for the specimen that was sequenced. Vertical lines represent genetically identical viruses; horizontal lines represent genetic descendants with additional SNVs. All sequenced specimens are classified as the SARS-CoV-2 B.1.617.2 (Delta) variant.

Following the outbreak, infected persons were isolated for 10 days after onset of symptoms (or positive test date for asymptomatic cases). All students with known exposure to an infected person quarantined at home for 10 days following their last known contact. Unvaccinated household and community contacts were directed to quarantine for 10 days following their last known exposure to an infected person, with the option to leave quarantine after 7 days if they remained asymptomatic and received a negative test result from a specimen collected on day 5 of quarantine or later. The two affected classrooms were closed and sanitized during May 21–30 and May 24–June 2, respectively.