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; 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 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 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

Biosciences

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

173 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
Early online date	24 May 2017
DOIs	https://doi.org/10.1038/nature22400
Publication status	Published - 15 Jun 2017

Keywords

Journal Article

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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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. Advance online publication. https://doi.org/10.1038/nature22400

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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.",

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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, KG, 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 G

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.

KW - Journal Article

U2 - 10.1038/nature22400

DO - 10.1038/nature22400

M3 - Article

C2 - 28538723

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

Keywords

UN SDGs

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