Multiple Introductions of Zika Virus into the United States Revealed through Genomic Epidemiology

Abstract : Zika virus (ZIKV) is currently causing an unprecedented pandemic linked to severe congenital syndromes1,2. In July 2016, mosquito-borne ZIKV transmission was first reported in the continental United States and since then, hundreds of locally acquired infections have been described3. To gain insights into the timing, source, and likely route(s) of introduction into the United States, we tracked the virus from its first detection in Miami, Florida by direct sequencing of ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We detected at least four distinct ZIKV introductions and estimate that 11-52 introductions contributed to the outbreak in Florida. Furthermore, our data suggests that ZIKV transmission likely started in the spring of 2016 - several months before initial detection. By analyzing epidemiological, surveillance, and genetic data, we discovered that several spatially distinct ZIKV transmission zones were likely portions of the same outbreak, rather than isolated events. Our analyses show that most introductions are linked to the Caribbean, which is supported by the high incidence rates and traffic, especially via cruises, from the region into Miami. By comparing mosquito abundance and travel capacity across the United States, we find that southern Florida is especially vulnerable to ZIKV introductions and at risk of repeat occurrences. By tracking the virus from its initial introduction into the United States, we provide a deeper understanding of how ZIKV initiates and sustains transmission in new regions.