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.
Martin et al. (Mon,) studied this question.