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 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. 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

doi:10.1038/nature22400

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 BanieckiKayla 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. 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

Research output: Contribution to journal › Article › peer-review

268 Citations (Scopus)

Abstract

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 language	English
Pages (from-to)	401-405
Number of pages	5
Journal	Nature
Volume	546
Issue number	7658
DOIs	https://doi.org/10.1038/nature22400
Publication status	Published - 15 Jun 2017
Externally published	Yes

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Grubaugh, N. D., Ladner, J. T., Kraemer, M. U. G., Dudas, G., Tan, A. L., Gangavarapu, K., Wiley, M. R., White, S., Thézé, J., Magnani, D. M., Prieto, K., Reyes, D., Bingham, A. M., Paul, L. M., Robles-Sikisaka, R., Oliveira, G., Pronty, D., Barcellona, C. M., Metsky, H. C., ... Andersen, K. G. (2017). Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature, 546(7658), 401-405. https://doi.org/10.1038/nature22400

@article{8a1c7633440949ad847b2ce32661e583,

title = "Genomic epidemiology reveals multiple introductions of Zika virus into the United States",

abstract = "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.",

author = "Grubaugh, \{Nathan D.\} and Ladner, \{Jason T.\} and Kraemer, \{Moritz U.G.\} and Gytis Dudas and Tan, \{Amanda L.\} and Karthik Gangavarapu and Wiley, \{Michael R.\} and Stephen White and Julien Th{\'e}z{\'e} and Magnani, \{Diogo M.\} and Karla Prieto and Daniel Reyes and Bingham, \{Andrea M.\} and Paul, \{Lauren M.\} and Refugio Robles-Sikisaka and Glenn Oliveira and Darryl Pronty and Barcellona, \{Carolyn M.\} and Metsky, \{Hayden C.\} and Baniecki, \{Mary Lynn\} and Kayla Barnes and Bridget Chak and Freije, \{Catherine A.\} and Adrianne Gladden-Young and Andreas Gnirke and Cynthia Luo and Bronwyn MacInnis and Matranga, \{Christian B.\} and Park, \{Daniel J.\} and James Qu and Schaffner, \{Stephen F.\} and Christopher Tomkins-Tinch and West, \{Kendra L.\} and Winnicki, \{Sarah M.\} and Shirlee Wohl and Yozwiak, \{Nathan L.\} and Joshua Quick and Fauver, \{Joseph R.\} and Kamran Khan and Brent, \{Shannon E.\} and Reiner, \{Robert C.\} and Lichtenberger, \{Paola N.\} and Ricciardi, \{Michael J.\} and Bailey, \{Varian K.\} and Watkins, \{David I.\} and Cone, \{Marshall R.\} and Kopp, \{Edgar W.\} and Hogan, \{Kelly N.\} and Cannons, \{Andrew C.\} and Reynald Jean and Monaghan, \{Andrew J.\} and Garry, \{Robert F.\} and Loman, \{Nicholas J.\} and Faria, \{Nuno R.\} and Porcelli, \{Mario C.\} and Chalmers Vasquez and Nagle, \{Elyse R.\} and Cummings, \{Derek A.T.\} and Danielle Stanek and Andrew Rambaut and Mariano Sanchez-Lockhart and Sabeti, \{Pardis C.\} and Gillis, \{Leah D.\} and Michael, \{Scott F.\} and Trevor Bedford and Pybus, \{Oliver G.\} and Sharon Isern and Gustavo Palacios and Andersen, \{Kristian G.\}",

year = "2017",

month = jun,

day = "15",

doi = "10.1038/nature22400",

language = "English",

volume = "546",

pages = "401--405",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7658",

}

Grubaugh, ND, Ladner, JT, Kraemer, MUG, Dudas, G, Tan, AL, Gangavarapu, K, Wiley, MR, White, S, Thézé, J, Magnani, DM, Prieto, K, Reyes, D, Bingham, AM, Paul, LM, Robles-Sikisaka, R, Oliveira, G, Pronty, D, Barcellona, CM, Metsky, HC, Baniecki, ML, Barnes, K, Chak, B, Freije, CA, Gladden-Young, A, Gnirke, A, Luo, C, MacInnis, B, Matranga, CB, Park, DJ, Qu, J, Schaffner, SF, Tomkins-Tinch, C, West, KL, Winnicki, SM, Wohl, S, Yozwiak, NL, Quick, J, Fauver, JR, Khan, K, Brent, SE, Reiner, RC, Lichtenberger, PN, Ricciardi, MJ, Bailey, VK, Watkins, DI, Cone, MR, Kopp, EW, Hogan, KN, Cannons, AC, Jean, R, Monaghan, AJ, Garry, RF, Loman, NJ, Faria, NR, Porcelli, MC, Vasquez, C, Nagle, ER, Cummings, DAT, Stanek, D, Rambaut, A, Sanchez-Lockhart, M, Sabeti, PC, Gillis, LD, Michael, SF, Bedford, T, Pybus, OG, Isern, S, Palacios, G & Andersen, KG 2017, 'Genomic epidemiology reveals multiple introductions of Zika virus into the United States', Nature, vol. 546, no. 7658, pp. 401-405. https://doi.org/10.1038/nature22400

TY - JOUR

T1 - Genomic epidemiology reveals multiple introductions of Zika virus into the United States

AU - Grubaugh, Nathan D.

AU - Ladner, Jason T.

AU - Kraemer, Moritz U.G.

AU - Dudas, Gytis

AU - Tan, Amanda L.

AU - Gangavarapu, Karthik

AU - Wiley, Michael R.

AU - White, Stephen

AU - Thézé, Julien

AU - Magnani, Diogo M.

AU - Prieto, Karla

AU - Reyes, Daniel

AU - Bingham, Andrea M.

AU - Paul, Lauren M.

AU - Robles-Sikisaka, Refugio

AU - Oliveira, Glenn

AU - Pronty, Darryl

AU - Barcellona, Carolyn M.

AU - Metsky, Hayden C.

AU - Baniecki, Mary Lynn

AU - Barnes, Kayla

AU - Chak, Bridget

AU - Freije, Catherine A.

AU - Gladden-Young, Adrianne

AU - Gnirke, Andreas

AU - Luo, Cynthia

AU - MacInnis, Bronwyn

AU - Matranga, Christian B.

AU - Park, Daniel J.

AU - Qu, James

AU - Schaffner, Stephen F.

AU - Tomkins-Tinch, Christopher

AU - West, Kendra L.

AU - Winnicki, Sarah M.

AU - Wohl, Shirlee

AU - Yozwiak, Nathan L.

AU - Quick, Joshua

AU - Fauver, Joseph R.

AU - Khan, Kamran

AU - Brent, Shannon E.

AU - Reiner, Robert C.

AU - Lichtenberger, Paola N.

AU - Ricciardi, Michael J.

AU - Bailey, Varian K.

AU - Watkins, David I.

AU - Cone, Marshall R.

AU - Kopp, Edgar W.

AU - Hogan, Kelly N.

AU - Cannons, Andrew C.

AU - Jean, Reynald

AU - Monaghan, Andrew J.

AU - Garry, Robert F.

AU - Loman, Nicholas J.

AU - Faria, Nuno R.

AU - Porcelli, Mario C.

AU - Vasquez, Chalmers

AU - Nagle, Elyse R.

AU - Cummings, Derek A.T.

AU - Stanek, Danielle

AU - Rambaut, Andrew

AU - Sanchez-Lockhart, Mariano

AU - Sabeti, Pardis C.

AU - Gillis, Leah D.

AU - Michael, Scott F.

AU - Bedford, Trevor

AU - Pybus, Oliver G.

AU - Isern, Sharon

AU - Palacios, Gustavo

AU - Andersen, Kristian G.

PY - 2017/6/15

Y1 - 2017/6/15

N2 - 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.

AB - 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.

U2 - 10.1038/nature22400

DO - 10.1038/nature22400

M3 - Article

SN - 0028-0836

VL - 546

SP - 401

EP - 405

JO - Nature

JF - Nature

IS - 7658

ER -

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

Abstract

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