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    • Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities1, 2. 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 Florida3, 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 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.
    • Genomic epidemiology reveals multiple introductions of Zika virus into the United States 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 Joshua Quick Joseph R. Fauver Kamran Khan Shannon E. Brent Robert C. Reiner Jr Paola N. Lichtenberger Michael J. Ricciardi Varian K. Bailey David I. Watkins Marshall R. Cone Edgar W. Kopp IV Kelly N. Hogan Andrew C. Cannons Reynald Jean Andrew J. Monaghan Robert F. Garry Nicholas J. Loman 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 Affiliations Contributions Corresponding authors Nature   (2017)   doi:10.1038/nature22400 Received   01 February 2017  Accepted   28 April 2017  Published online   24 May 2017 These authors contributed equally to this work. Nathan D. Grubaugh,  Jason T. Ladner,  Moritz U. G. Kraemer,  Gytis Dudas,  Amanda L. Tan, Karthik Gangavarapu,  Michael R. Wiley,  Stephen White &  Julien Thézé These authors jointly supervised this work. Pardis C. Sabeti,  Leah D. Gillis,  Scott F. Michael,  Trevor Bedford,  Oliver G. Pybus,  Sharon Isern, Gustavo Palacios &  Kristian G. Andersen Affiliations Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA Nathan D. Grubaugh,   Karthik Gangavarapu,   Refugio Robles-Sikisaka &   Kristian G. Andersen Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland 21702, USA Jason T. Ladner,   Michael R. Wiley,   Karla Prieto,   Daniel Reyes,   Elyse R. Nagle,   Mariano Sanchez-Lockhart &   Gustavo Palacios Department of Zoology, University of Oxford, Oxford OX1 3PS, UK Moritz U. G. Kraemer,   Julien Thézé,   Nuno R. Faria &   Oliver G. Pybus Boston Children’s Hospital, Boston, Massachusetts 02115, USA Moritz U. G. Kraemer Harvard Medical School, Boston, Massachusetts 02115, USA Moritz U. G. Kraemer Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA Gytis Dudas &   Trevor Bedford Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida 33965, USA Amanda L. Tan,   Lauren M. Paul,   Carolyn M. Barcellona,   Scott F. Michael &   Sharon Isern College of Public Health, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA Michael R. Wiley &   Karla Prieto Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, Florida 33125, USA Stephen White,   Darryl Pronty &   Leah D. Gillis Department of Pathology, University of Miami Miller School of Medicine, Miami, Florida 33136, USA Diogo M. Magnani,   Michael J. Ricciardi,   Varian K. Bailey &   David I. Watkins Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA Daniel Reyes,   Elyse R. Nagle &   Mariano Sanchez-Lockhart Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida 32399, USA Andrea M. Bingham &   Danielle Stanek Scripps Translational Science Institute, La Jolla, California 92037, USA Glenn Oliveira &   Kristian G. Andersen The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA 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 &   Pardis C. Sabeti Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK Joshua Quick &   Nicholas J. Loman Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA Joseph R. Fauver Li Ka Shing Knowledge Institute, St Michael’s Hospital, Toronto, Ontario M5B 1T8, Canada Kamran Khan &   Shannon E. Brent Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada Kamran Khan Institute for Health Metrics and Evaluation, University of Washington, Seattle, Washington 98121, USA Robert C. Reiner Jr Division of Infectious Diseases, University of Miami Miller School of Medicine, Miami, Florida 33136, USA Paola N. Lichtenberger Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida 33612, USA Marshall R. Cone,   Edgar W. Kopp IV,   Kelly N. Hogan &   Andrew C. Cannons Florida Department of Health in Miami-Dade County, Miami, Florida 33125, USA Reynald Jean National Center for Atmospheric Research, Boulder, Colorado 80307, USA Andrew J. Monaghan Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana 70112, USA Robert F. Garry Miami-Dade County Mosquito Control, Miami, Florida 33178, USA Mario C. Porcelli &   Chalmers Vasquez Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610, USA Derek A. T. Cummings Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK Andrew Rambaut Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA Andrew Rambaut Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA Pardis C. Sabeti Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts 02115, USA Pardis C. Sabeti Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA Pardis C. Sabeti Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA Kristian G. Andersen Contributions All contributions are listed in order of authorship. Designed the experiments: N.D.G., J.T.L., G.D., M.U.G.K., D.A.T.C., P.C.S., L.D.G., S.F.M., T.B., O.G.P., S.I., G.P., and K.G.A. Collected samples: A.L.T., S.W., D.M.M., A.M.B., L.M.P., D.P., C.M.B., P.N.L., M.J.R., V.K.B., D.I.W., M.R.C., E.W.K., K.N.H., A.C.C., R.J., M.C.P., C.V., D.S., L.D.G., S.F.M., and S.I. Performed the sequencing: N.D.G., M.R.W., K.P., D.R., R.R.-S., G.O., and E.R.N. Provided data, reagents, or protocols: N.D.G., J.T.L., G.D., M.U.G.K., K.G., M.R.W., R.R.-S., G.O., H.C.M., M.L.B., K.G.B., B.C., C.A.F., A.G.-Y., A.G., C.L., B.M., C.B.M., D.J.P., J. Q.U, S.F.S., C.T.-T., K.L.W., S.M.W., S.W., N.L.Y., J.Qui., J.R.F., K.K., S.E.B., A.J.M., R.F.G., N.J.L., M.C.P., C.V., P.C.S., S.F.M., and S.I. Analysed the data: N.D.G., J.T.L., G.D., M.U.G.K., K.G., J.T., J.R.F., R.C.R., N.R.F., D.A.T.C., A.R., M.S.-L., T.B., S.F.M, O.G.P., S.I., and K.G.A. Edited manuscript: G.D., M.U.G.K., J.T., S.F.S., A.R., T.B., O.G.P., S.I., and G.P. Wrote manuscript: N.D.G., J.T.L., and K.G.A. All authors read and approved the manuscript.
    • Nature paper describing the multiple Zika introductions into Florida has been published Genomic epidemiology reveals multiple introductions of Zika virus into the United States http://www.nature.com/nature/journal/vaop/ncurrent/full/nature22400.html    
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