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

ImportanceThe 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. ObjectiveTo determine whether high vaccination coverage can mitigate the spread of SARS-CoV-2, even in the presence of highly-transmissible variants and congregate living. SettingThis study was conducted at a mid-sized midwestern university during the spring 2021 semester. DesignThe 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. ParticipantsThis study includes 14,894 individuals from the university population who tested on campus for COVID-19 during the spring 2021 semester. Main Outcomes and MeasuresPositive 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. ResultsBetween 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 RelevanceThis study demonstrates the high effectiveness of robust vaccination programs even in the presence of highly-transmissible variants and congregate living. KEY POINTSO_ST_ABSQuestionC_ST_ABSHow is the spread of COVID-19 affected by increasing rates of vaccination? FindingsWe leverage 190,000+ COVID-19 surveillance tests including 1,603 positives for COVID-19 at a mid-sized midwestern university from January 6 - May 20, 2021. Genomic sequencing indicates that the Alpha (B.1.1.7) variant was first identified in early February and became the dominant variant by early March and the only variant resulting in positive cases by April. An increase in vaccination was associated with a dramatic decrease in COVID-19 cases in the campus population. MeaningMass vaccination efforts can effectively control the spread of SARS-CoV-2 even as highly-transmissible variants are introduced.

Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling (preprint)

ABSTRACT Accurate tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been critical in efforts to control its spread. The accuracy of molecular tests for SARS-CoV-2 has been assessed numerous times, usually in reference to a gold standard diagnosis. One major disadvantage of that approach is the possibility of error due to inaccuracy of the gold standard, which is especially problematic for evaluating testing in a real-world surveillance context. We used an alternative approach known as Bayesian latent class modeling (BLCM), which circumvents the need to designate a gold standard by simultaneously estimating the accuracy of multiple tests. We applied this technique to a collection of 1,716 tests of three types applied to 853 individuals on a university campus during a one-week period in October 2020. We found that reverse transcriptase polymerase chain reaction (RT-PCR) testing of saliva samples performed at a campus facility had higher sensitivity (median: 0.923; 95% credible interval: 0.732-0.996) than RT-PCR testing of nasal samples performed at a commercial facility (median: 0.859; 95% CrI: 0.547-0.994). The reverse was true for specificity, although the specificity of saliva testing was still very high (median: 0.993; 95% CrI: 0.983-0.999). An antigen test was less sensitive and specific than both of the RT-PCR tests. These results suggest that RT-PCR testing of saliva samples at a campus facility can be an effective basis for surveillance screening to prevent SARS-CoV-2 transmission in a university setting.