Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital syndromes(1,2). In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States and since then, hundreds of locally-acquired infections have been reported in Florida(3,4). To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least four introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission likely started in the spring of 2016 - several months before initial detection. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions are linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.