SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

Abstract

Background: We aimed to evaluate a testing program to facilitate control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission at a large university and measure spread in the university community using viral genome sequencing.

Methods: Our prospective longitudinal study used remote contactless enrollment, daily mobile symptom and exposure tracking, and self-swab sample collection. Individuals were tested if the participant was exposed to a known SARS-CoV-2-infected person, developed new symptoms, or reported high-risk behavior (such as attending an indoor gathering without masking or social distancing), if a member of a group experiencing an outbreak, or at enrollment. Study participants included students, staff, and faculty at an urban public university during the Autumn quarter of 2020.

Results: We enrolled 16 476 individuals, performed 29 783 SARS-CoV-2 tests, and detected 236 infections. Seventy-five percent of positive cases reported at least 1 of the following: symptoms (60.8%), exposure (34.7%), or high-risk behaviors (21.5%). Greek community affiliation was the strongest risk factor for testing positive, and molecular epidemiology results suggest that specific large gatherings were responsible for several outbreaks.

Conclusions: A testing program focused on individuals with symptoms and unvaccinated persons who participate in large campus gatherings may be effective as part of a comprehensive university-wide mitigation strategy to control the spread of SARS-CoV-2.

Keywords: COVID-19 testing; SARS-CoV-2; genome sequencing; outbreak; university.

Figure 1.

Daily attestation survey engagement over time. A, Number of daily attestations completed during the study period. Between October 11 and 13, 2020, we experienced an outage of the text messaging service used to send daily attestation survey invites, and this resulted in a reduced response rate. B, Positive daily attestations stratified by reason for positive attestation. A marked increase in positive attestations was observed the day after Halloween, when 487 reported gathering, a 4.7-fold increase from the mean daily gathering attestation positive of 105.

Figure 2.

Comparison of viral loads in symptomatic (n = 124) vs presymptomatic (n = 48) positive and inconclusive samples. Cycle thresholds for samples (each represented by 1 dot) tested using our protocol with nucleic acid extraction (before November 18) are shown here. Complete data are shown in Supplementary Figure 6. Box plots show the median values and 25th and 75th percentiles, with vertical lines demonstrating the range of values. Abbreviations: Ct, cycle threshold; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 3.

Dynamics of a Greek community outbreak. A, Percent positivity over time of university groups and the surrounding county. The employee category includes university staff and faculty, and the Greek-affiliated students category includes all Greek-affiliated students including those living in Greek houses, Greek off-campus housing, and Greek-affiliated dorm residents. B, Greek chapter-level SARS-CoV-2 outbreak dynamics; counts of cases identified by chapter during the Autumn quarter. Sororities are shown in blue and fraternities in red. Chapters with no infections detected (n = 20) or ≤2 infections detected (n = 5) are not shown. C, Example of chapter-level individual SARS-CoV-2 outbreak dynamics within 1 Greek chapter (ending on November 2). Lines represent individual study participants tested multiple times, and dots signify a single test. Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 3.

Dynamics of a Greek community outbreak. A, Percent positivity over time of university groups and the surrounding county. The employee category includes university staff and faculty, and the Greek-affiliated students category includes all Greek-affiliated students including those living in Greek houses, Greek off-campus housing, and Greek-affiliated dorm residents. B, Greek chapter-level SARS-CoV-2 outbreak dynamics; counts of cases identified by chapter during the Autumn quarter. Sororities are shown in blue and fraternities in red. Chapters with no infections detected (n = 20) or ≤2 infections detected (n = 5) are not shown. C, Example of chapter-level individual SARS-CoV-2 outbreak dynamics within 1 Greek chapter (ending on November 2). Lines represent individual study participants tested multiple times, and dots signify a single test. Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 4.

Molecular epidemiology of a university outbreak. A, Phylogenetic tree of SARS-CoV-2 samples from Washington, including 88 samples from this study. Included here are all SARS-CoV-2 genomes from Washington collected on or after September 25, 2020, a random subsample of 1000 Washington samples collected before September 25, and the Wuhan/Hu-1 reference genome. Samples are positioned on the x-axis by date of collection. B, Detail of a cluster of university genomes organized horizontally by collection date and (C) by divergence, or the number of genetic changes relative to the SARS-CoV-2 reference genome. Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 4.

Molecular epidemiology of a university outbreak. A, Phylogenetic tree of SARS-CoV-2 samples from Washington, including 88 samples from this study. Included here are all SARS-CoV-2 genomes from Washington collected on or after September 25, 2020, a random subsample of 1000 Washington samples collected before September 25, and the Wuhan/Hu-1 reference genome. Samples are positioned on the x-axis by date of collection. B, Detail of a cluster of university genomes organized horizontally by collection date and (C) by divergence, or the number of genetic changes relative to the SARS-CoV-2 reference genome. Abbreviation: SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.