Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread

Authors:

Gage K. Moreno^1*, Katarina M. Braun^2*, Kasen K. Riemersma^2*, Michael A. Martin^3,4, Peter J. Halfmann^2,5, Chelsea M Crooks², Trent Prall¹, David Baker¹, John J. Baczenas^1,6, Anna S. Heffron¹, Mitchell Ramuta¹, Manjeet Khubbar⁷, Andrea M. Weiler^2,6, Molly A. Accola⁸, William M Rehrauer⁸, Shelby L. O’Connor^1,6, Nasia Safdar⁹, Caitlin S. Pepperell^9,10, Trivikram Dasu⁷, Sanjib Bhattacharyya⁷, Yoshihiro Kawaoka^2,5, Katia Koelle³, David H. O’Connor^1#, Thomas C. Friedrich^2,6#

*These authors contributed equally

#These authors contributed equally

¹Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, United States of America

²Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, United States of America

³Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, United States of America

⁴Department of Biology, Emory University, Atlanta, GA, United States of America

⁵Influenza Research Institute, School of Veterinary Sciences, University of Wisconsin-Madison, Madison, WI, United States

⁶Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI, United States of America

⁷City of Milwaukee Health Department Laboratory, Milwaukee, WI, United States of America

⁸University of Wisconsin School of Medicine and Public Health, Madison, WI, United States of America and the William S. Middleton Memorial Veterans Hospital

⁹Department of Medicine, Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI

¹⁰Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, United States of America

Abstract

Evidence-based public health approaches that minimize the introduction and spread of new SARS-CoV-2 transmission clusters are urgently needed in the United States and other countries struggling with expanding epidemics. Here we analyze 247 full-genome SARS-CoV-2 sequences from two nearby communities in Wisconsin, USA, and find surprisingly distinct patterns of viral spread. Dane County had the 12th known introduction of SARS-CoV-2 in the United States, but this did not lead to descendant community spread. Instead, the Dane County outbreak was seeded by multiple later introductions, followed by limited community spread. In contrast, relatively few introductions in Milwaukee County led to extensive community spread. We present evidence for reduced viral spread in both counties following the statewide “Safer at Home” order, which went into effect 25 March 2020. Our results suggest patterns of SARS-CoV-2 transmission may vary substantially even in nearby communities. Understanding these local patterns will enable better targeting of public health interventions.