by Chaney C. Kalinich, Cole G. Jensen, Peter Neugebauer, Mary E. Petrone, Mario Peña-Hernández, Isabel M. Ott, Anne L. Wyllie, Tara Alpert, Chantal B. F. Vogels, Joseph R. Fauver, Nathan D. Grubaugh, Anderson F. Brito
Genomic epidemiology can provide a unique, real-time understanding of SARS-CoV-2 transmission patterns. Yet the potential for genomic analyses to guide local policy and community-based behavioral decisions is limited because they are often oriented towards specially trained scientists and conducted on a national or global scale. Here, we propose a new paradigm: Phylogenetic analyses performed on a local level (municipal, county, or state), with results communicated in a clear, timely, and actionable manner to strengthen public health responses. We believe that presenting results rapidly, and tailored to a non-expert audience, can serve as a template for effective public health response to COVID-19 and other emerging viral diseases.