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

Research output: Contribution to journalArticlepeer-review


  • Nathan D Grubaugh
  • Jason T Ladner
  • Moritz U G Kraemer
  • Gytis Dudas
  • Amanda L Tan
  • Karthik Gangavarapu
  • Michael R Wiley
  • Stephen White
  • Julien Thézé
  • Diogo M Magnani
  • Karla Prieto
  • Daniel Reyes
  • Andrea M Bingham
  • Lauren M Paul
  • Refugio Robles-Sikisaka
  • Glenn Oliveira
  • Darryl Pronty
  • Carolyn M Barcellona
  • Hayden C Metsky
  • Mary Lynn Baniecki
  • Kayla G Barnes
  • Bridget Chak
  • Catherine A Freije
  • Adrianne Gladden-Young
  • Andreas Gnirke
  • Cynthia Luo
  • Bronwyn MacInnis
  • Christian B Matranga
  • Daniel J Park
  • James Qu
  • Stephen F Schaffner
  • Christopher Tomkins-Tinch
  • Kendra L West
  • Sarah M Winnicki
  • Shirlee Wohl
  • Nathan L Yozwiak
  • Joseph R Fauver
  • Kamran Khan
  • Shannon E Brent
  • Robert C Reiner
  • Paola N Lichtenberger
  • Michael J Ricciardi
  • Varian K Bailey
  • David I Watkins
  • Marshall R Cone
  • Edgar W Kopp
  • Kelly N Hogan
  • Andrew C Cannons
  • Reynald Jean
  • Andrew J Monaghan
  • Robert F Garry
  • Nuno R Faria
  • Mario C Porcelli
  • Chalmers Vasquez
  • Elyse R Nagle
  • Derek A T Cummings
  • Danielle Stanek
  • Andrew Rambaut
  • Mariano Sanchez-Lockhart
  • Pardis C Sabeti
  • Leah D Gillis
  • Scott F Michael
  • Trevor Bedford
  • Oliver G Pybus
  • Sharon Isern
  • Gustavo Palacios
  • Kristian G Andersen

Colleges, School and Institutes

External organisations

  • The Scripps Research Institute, Department of Immunology and Microbial Science, La Jolla, California 92037, USA.
  • Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland 21702, USA.
  • Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK.
  • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
  • Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA.
  • Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA.
  • Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.
  • Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA.
  • Scripps Translational Science Institute, La Jolla, California 92037, USA.
  • The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
  • Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
  • Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA.
  • Li Ka Shing Knowledge Institute, St Michael's Hospital, Toronto, Ontario M5B 1T8, Canada.
  • Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington 98121, USA.
  • Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida 33136, USA.
  • Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA.
  • Florida Department of Health in Miami-Dade County, Miami, Florida 33125, USA.
  • National Center for Atmospheric Research, Boulder, Colorado 80307, USA.
  • Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA.
  • Miami-Dade County Mosquito Control, Miami, Florida 33178, USA.
  • Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, USA.
  • Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Edinburgh EH9 3FL, UK.


Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. 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 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were 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.


Original languageEnglish
Pages (from-to)401-405
Number of pages5
Issue number7658
Early online date24 May 2017
Publication statusPublished - 15 Jun 2017


  • Journal Article