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 Theze; 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; 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; Nicholas J Loman; Nuno R Faria; Mario C Porcelli; Chalmers Vasquez; Elyse R. N Agle; 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

doi:10.1038/nature22400

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

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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 Theze, Diogo M Magnani, …

Nature (London), Vol.546(7658), pp.401-405

06-15-2017

DOI: https://doi.org/10.1038/nature22400

PMCID: PMC5536180

PMID: 28538723

Appears in United Nations Sustainable Development Goals @ FGCU

Abstract

Multidisciplinary Sciences

Science & Technology

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Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities(1,2). 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 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 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.

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Title: Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Creators: Nathan D Grubaugh - Scripps Research Institute
Jason T Ladner - United States Army Medical Research Institute of Infectious Diseases
Moritz U. G Kraemer - University of Oxford
Gytis Dudas - Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
Amanda L Tan - Florida Gulf Coast University
Karthik Gangavarapu - Scripps Research Institute
Michael R Wiley - US Army Med Res Inst Infect Dis, Ctr Genome Sci, Ft Detrick, MD 21702 USA
Stephen White - Florida Department of Health
Julien Theze - University of Oxford
Diogo M Magnani - University of Miami
Karla Prieto - University of Nebraska Medical Center
Daniel Reyes - University of Nebraska Medical Center
Andrea M Bingham - Scripps Health
Lauren M Paul - Florida Gulf Coast University
Refugio Robles-Sikisaka - Scripps Research Institute
Glenn Oliveira - Scripps Health
Darryl Pronty - Florida Department of Health
Carolyn M Barcellona - Florida Gulf Coast University
Hayden C Metsky - Broad Institute
Mary Lynn Baniecki - Broad Institute
Kayla G Barnes - Broad Institute
Bridget Chak - Broad Institute
Catherine A Freije - Broad Institute
Adrianne Gladden-Young - Broad Institute
Andreas Gnirke - Broad Institute
Cynthia Luo - Broad Institute
Bronwyn MacInnis - Broad Institute
Christian B Matranga - Broad Institute
Daniel J Park - Broad Institute
James Qu - Broad Institute
Stephen F Schaffner - Broad Institute
Christopher Tomkins-Tinch - Broad Institute
Kendra L West - Broad Institute
Sarah M Winnicki - Broad Institute
Shirlee Wohl - Broad Institute
Nathan L Yozwiak - Broad Institute
Joshua Quick - University of Birmingham
Joseph R Fauver - Colorado State University
Kamran Khan - University of Toronto
Shannon E Brent - University of Toronto
Robert C Reiner - University of Washington
Paola N Lichtenberger - University of Miami
Michael J Ricciardi - University of Miami
Varian K Bailey - University of Miami
David I Watkins - University of Miami
Marshall R Cone - Florida Department of Health
Edgar W Kopp - Florida Department of Health
Kelly N Hogan - Florida Department of Health
Andrew C Cannons - Florida Department of Health
Reynald Jean - Florida Department of Health
Andrew J Monaghan - NSF National Center for Atmospheric Research
Robert F Garry - Tulane University
Nicholas J Loman - University of Birmingham
Nuno R Faria - University of Oxford
Mario C Porcelli - Miami Dade Cty Mosquito Control, Miami, FL 33178 USA
Chalmers Vasquez - Miami Dade Cty Mosquito Control, Miami, FL 33178 USA
Elyse R. N Agle - Univ Nebraska Med Ctr, Dept Pathol & Microbiol, Omaha, NE 68198 USA
Derek A. T Cummings - University of Florida
Danielle Stanek - Florida Department of Health
Andrew Rambaut - University of Edinburgh
Mariano Sanchez-Lockhart - US Army Med Res Inst Infect Dis, Ctr Genome Sci, Ft Detrick, MD 21702 USA
Pardis C Sabeti - Broad Institute
Leah D Gillis - Florida Department of Health
Scott F Michael - Florida Gulf Coast University
Trevor Bedford - Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
Oliver G Pybus - University of Oxford
Sharon Isern - Florida Gulf Coast University
Gustavo Palacios - United States Army Medical Research Institute of Infectious Diseases
Kristian G Andersen - Scripps Research Institute
Publication Details: Nature (London), Vol.546(7658), pp.401-405
Publisher: NATURE PUBLISHING GROUP; BERLIN
Number of pages: 20
Grant note: MR/L015080/1 / Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC); European Commission R35GM119774 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) S10OD020069 / OFFICE OF THE DIRECTOR, NATIONAL INSTITUTES OF HEALTH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA U01CK000510 / CDC; United States Department of Health & Human Services; Centers for Disease Control & Prevention - USA U54-GM088491 / US NIH MIDAS program; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA Howard Hughes Medical Institute; Howard Hughes Medical Institute UL1TR001114 / NIH NCATS CTSA; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Center for Advancing Translational Sciences (NCATS) 614725-PATHPHYLODYN / EU ERC; European Research Council (ERC); European Commission Broad Institute BroadNext10 program U19AI115589 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) UL1TR000460 / NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Center for Advancing Translational Sciences (NCATS) Mahan Postdoctoral Fellowship from the Computational Biology Program at Fred Hutch AWS Cloud Credits for Research 278433-PREDEMICS / EU; European Commission Ray Thomas Foundation HHSN272201400048C / NIAID; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) 6U01CK000510-01M001 / ALLCDC; United States Department of Health & Human Services; Centers for Disease Control & Prevention - USA 643476-COMPARE / Horizon grant 260864 / ERC; European Research Council (ERC); European Commission 5T32AI007244-33; R35 GM11977401 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA AID-OAA-A-14-00102 / USAID Emerging Pandemic Threats Program-2 PREDICT-2; United States Agency for International Development (USAID) 204311/Z/16/Z / Sir Henry Dale Fellowship ASTMH Shope Fellowship MR/L015080/1 / MRC; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) U19AI110818; R01AI099210 / NIH NIAID; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) DARPA; United States Department of Defense; Defense Advanced Research Projects Agency (DARPA)
Identifiers: 99383436588006570
Academic Unit: Department of Biological Sciences
Language: English
Resource Type: Journal article

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

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