SARS-CoV-2 Variant Tracking and Mitigation: Strategies and Results from In-Person Learning at a Midwestern University in the 2020/2021 School Year

Abstract

Importance. The COVID—19 pandemic led many higher education institutions to close campuses during the 2020—21 academic year. As campuses prepared for a return to in—person education, many institutions were mandating vaccines for students and considering the same for faculty and staff. This paper demonstrates the effectiveness of such a strategy based on evidence from a mid—sized midwestern university. Objective. To determine whether high vaccination coverage can mitigate the spread of SARS—CoV—2, even in the presence of highly—transmissible variants and congregate living. Setting: This study was conducted at a mid—sized midwestern university during the spring 2021 semester. Design: The university developed a saliva-based surveillance program capable of high—throughput SARS—CoV—2 polymerase chain reaction testing and genomic sequencing with the capacity to deliver results in less than 24 hours. On April 7, 2021, the university announced a vaccine requirement for all students for the fall 2021 semester and announced the same requirement for faculty and staff on May 20, 2021. The university hosted an onsite mass vaccination clinic using the two—dose Pfizer—BioNTech vaccine April 8—15 and April 29—May 6, 2021. Data from January 6—May 20, 2021 were analyzed. Participants: This study includes 14,894 individuals from the university population who tested on campus for COVID—19 during the spring 2021 semester. Main Outcomes and Measures. Positive SARS—CoV—2 diagnosis was confirmed by quantitative reverse transcription—polymerase chain reaction (qRT—PCR) of saliva specimens and variant identity was assessed by qRT—PCR and next—generation sequencing (NGS) of viral genomes. Results. Between January and May 2021, the university conducted 196,185 COVID—19 tests and identified 1,603 positives — ~89% students — with 687 identified via PCR of saliva specimens. The Alpha (B.1.1.7) variant constituted 44% of total positives sequenced. By May 20, 2021, 91% (10,068) of students, 92% (814) of faculty, and 72% (2,081) of staff were vaccinated. The 7—day rolling average of positive cases peaked at 37 cases on February 17 but declined to zero by May 14, 2021. The 7—day moving average of positive cases was inversely associated with the cumulative vaccination rate. Conclusions and Relevance. This study demonstrates the high effectiveness of robust vaccination programs even in the presence of highly—transmissible variants and congregate living.

Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant

“…Overall, we were able to successfully achieve viral genomic sequencing of an average of 32% of weekly cases confirmed SARS-CoV-2 positive by RT-PCR throughout the study period. This percentage is consistent with other studies conducted in a university setting, and higher than other studies done in a similarly localized population or state-level sequencing efforts in states like New York which aims to sequence 15% of weekly samples to pick up trends over time [16,19,20,45]. A total of 677 whole-genomes were successfully sequenced from the Purdue campus over the course of the 18-week study period, taking into account differences in actual case number positivity and testing per week in the community.…”

“…While rapid implementation of SARS-CoV-2 genome sequencing has proven useful in the investigation of COVID-19 dynamics in other institutional settings like healthcare, few studies have been conducted on university campuses [15][16][17][18][19][20][21][22][23]. Some studies in the university setting have evaluated testing programs to understand control of SARS-CoV-2 transmission, while others used modeling approaches to infer SARS-CoV-2 transmission or estimate the introduction and growth rate of particular variants [17,[24][25][26].…”

“…The plan also included active surveillance with weekly random testing by anterior nasal swabs and RT-PCR of approximately 10% of the on-campus student and employee population -a combination of mitigation strategies that were readily applied in many institutions with some degree of in-person instruction [14]. Importantly, however, little genomic evidence has been collected to understand campus transmission in general and the effects of mitigation efforts in particular [14][15][16][17].…”