Evaluation of SARS-CoV-2 response at the University of North Carolina (UNC) at Charlotte using percent positivity data and viral genomic sequence data

In this paper, we use two datasets: 1) percent positivity data based on real-time PCR testing of students on the UNC Charlotte campus and in the surrounding County, Mecklenburg, North Carolina) and 2) nucleotide sequence data from SARS-CoV-2 isolates from students who tested positive and similar background data collected globally and submitted to The National Center for Biotechnology Information, (NCBIGenBank). We develop graphical and phylogenetic means to assess the disease mitigation efforts over time. These efforts included the early warning of wastewater surveillance, the encouragement of vaccination, intensive testing, contract tracing, and isolation of infected students. Based on the percent positivity data, we conclude that there were periods in which the measured percent positivity of SARS-CoV-2 was worse on campus than in the surrounding county and periods where measured percent positivity was worse throughout the county than on campus. The viral phylogeny based on sequence data shows that there was not a long coherent epidemic on campus. It was impossible to keep the virus from coming on campus. The virus invaded the campus multiple independent times, but each time it did not spread due to the disease mitigation efforts of the campus. One exception is a large clade of campus cases during the Omicron surge.