Containment of a Multi-index B.1.1.7 Outbreak on a University Campus Through a Genomically Informed Public Health Response

Abstract Increasing the precision of outbreak containment for emerging virus strains requires real-time virus identification that can be integrated with specific public health actions. During the SARS-CoV-2 pandemic, we established a multisector partnership to support rapid genomically informed containment response. This system was in place prior to emergence of the first cluster of SARS-CoV-2 cases with lineage B.1.1.7 in the state of Michigan, which was identified through intensive university-led surveillance sampling and rapid, targeted sequencing. Sequencing data were integrated in real time with a collaborative investigation and response led by the local and state health departments, with university and athletic medicine COVID-19 response teams. In this response, subsequent sampling and just-in-time sequencing were specifically directed toward first- and second-order contacts of B.1.1.7 cases. A total of 50 cases of B.1.1.7-lineage SARS-CoV-2 were identified in this outbreak, which was due to 3 coincident introductions of B.1.1.7-lineage SARS-CoV-2 in the background of a large number of non-B.1.1.7 cases. This initial outbreak was contained, as all subsequent B.1.1.7 infections in the university and surrounding community were due to genetically distinct lineages. This investigation demonstrates the successful implementation of a genomically informed outbreak response that can be extended to university campuses and other settings at high risk for rapid emergence of new viruses or viral variants.