Genome sequencing reveals Zika virus diversity and spread in the Americas

Hayden C Metsky; Christian B Matranga; Shirlee Wohl; Stephen F. Schaffner; Catherine A Freije; Sarah Winnicki; Kendra West; J Qu; Mary Lynn Baniecki; Adrianne Gladden-Young; Aaron E. Lin; Tomkins-Tinch Christopher; S.H Ye; Daniel J Park; Cynthia Luo; Kayla G Barnes; R.R. Shah; Bridget Chak; G. Barbosa-Lima; E. Delatorre; Y.R. Vieira; Lauren M Paul; Amanda L Tan; Carolyn M Barcellona; Mario C Porcelli; Chalmers  Vasquez; Andrew C Cannons; Marshall R Cone; Kelly N Hogan; Edgar W Kopp IV; J.J. Anzinger; K.F. Garcia; L.A. Parhap; R.M. Gelvez Ramirez; Miranda Montoya; D.P. Rojas; C.M. Brown; S. Hennigan; B. Sabina; S. Scotland; K. Gangavarapu; N.D. Grubaugh; G. Oliveira; R. Robles-Sikisaka; Andrew Rambaut; L. Gehrke; S. Smole; M.E. Halloran; L.A. Villar Centeno; S. Mattar; I. Lorenzana; J.  Cerbino-Neto; C. Valim; W.  Degrave; P.T. Bozza; T.M.L. Souza; I. Bosch; N.L. Yozwiak; B.L. MacInnis; P.C. Sabeti

doi:10.1038/nature22402

Genome sequencing reveals Zika virus diversity and spread in the Americas

Hayden C Metsky, Christian B Matranga, Shirlee Wohl, Stephen F. Schaffner, Catherine A Freije, Sarah Winnicki, Kendra West, J Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E. Lin, Tomkins-Tinch Christopher, S.H Ye, Daniel J Park, Cynthia Luo, Kayla G Barnes, R.R. Shah, Bridget Chak, G. Barbosa-Lima, E. DelatorreY.R. Vieira, Lauren M Paul, Amanda L Tan, Carolyn M Barcellona, Mario C Porcelli, Chalmers Vasquez, Andrew C Cannons, Marshall R Cone, Kelly N Hogan, Edgar W Kopp IV, J.J. Anzinger, K.F. Garcia, L.A. Parhap, R.M. Gelvez Ramirez, Miranda Montoya, D.P. Rojas, C.M. Brown, S. Hennigan, B. Sabina, S. Scotland, K. Gangavarapu, N.D. Grubaugh, G. Oliveira, R. Robles-Sikisaka, Andrew Rambaut, L. Gehrke, S. Smole, M.E. Halloran, L.A. Villar Centeno, S. Mattar, I. Lorenzana, J. Cerbino-Neto, C. Valim, W. Degrave, P.T. Bozza, T.M.L. Souza, I. Bosch, N.L. Yozwiak, B.L. MacInnis, P.C. Sabeti

School of Biological Sciences

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

Abstract

Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

Original language	English
Pages (from-to)	411–415
Journal	Nature
Volume	546
DOIs	https://doi.org/10.1038/nature22402
Publication status	Published - 24 May 2017

Access to Document

10.1038/nature22402

Genome sequencing reveals Zika virus diversity and spread in the AmericasAccepted author manuscript, 1.61 MB

COMPARE: COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe
Woolhouse, M. (Principal Investigator)
EU government bodies
1/12/14 → 30/11/19
Project: Research
PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach
Rambaut, A. (Principal Investigator)
EU government bodies
1/11/11 → 30/04/17
Project: Research

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)
Rambaut, A. (Member)
Sept 2009 → Aug 2015
Activity: Membership types › Membership of external research organisation

Cite this

Metsky, H. C., Matranga, C. B., Wohl, S., Schaffner, S. F., Freije, C. A., Winnicki, S., West, K., Qu, J., Baniecki, M. L., Gladden-Young, A., Lin, AE., Christopher, T.-T., Ye, S. H., Park, D. J., Luo, C., Barnes, K. G., Shah, R. R., Chak, B., Barbosa-Lima, G., ... Sabeti, P. C. (2017). Genome sequencing reveals Zika virus diversity and spread in the Americas. Nature, 546, 411–415. https://doi.org/10.1038/nature22402

@article{8e61eebb00154a868bee0e00f9779df4,

title = "Genome sequencing reveals Zika virus diversity and spread in the Americas",

abstract = "Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.",

author = "Metsky, \{Hayden C\} and Matranga, \{Christian B\} and Shirlee Wohl and Schaffner, \{Stephen F.\} and Freije, \{Catherine A\} and Sarah Winnicki and Kendra West and J Qu and Baniecki, \{Mary Lynn\} and Adrianne Gladden-Young and Aaron E. Lin and Tomkins-Tinch Christopher and S.H Ye and Park, \{Daniel J\} and Cynthia Luo and Barnes, \{Kayla G\} and R.R. Shah and Bridget Chak and G. Barbosa-Lima and E. Delatorre and Y.R. Vieira and Paul, \{Lauren M\} and Tan, \{Amanda L\} and Barcellona, \{Carolyn M\} and Porcelli, \{Mario C\} and Chalmers Vasquez and Cannons, \{Andrew C\} and Cone, \{Marshall R\} and Hogan, \{Kelly N\} and \{Kopp IV\}, \{Edgar W\} and J.J. Anzinger and K.F. Garcia and L.A. Parhap and \{Gelvez Ramirez\}, R.M. and Miranda Montoya and D.P. Rojas and C.M. Brown and S. Hennigan and B. Sabina and S. Scotland and K. Gangavarapu and N.D. Grubaugh and G. Oliveira and R. Robles-Sikisaka and Andrew Rambaut and L. Gehrke and S. Smole and M.E. Halloran and \{Villar Centeno\}, L.A. and S. Mattar and I. Lorenzana and J. Cerbino-Neto and C. Valim and W. Degrave and P.T. Bozza and T.M.L. Souza and I. Bosch and N.L. Yozwiak and B.L. MacInnis and P.C. Sabeti",

year = "2017",

month = may,

day = "24",

doi = "10.1038/nature22402",

language = "English",

volume = "546",

pages = "411–415",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Publishing Group",

}

Metsky, HC, Matranga, CB, Wohl, S, Schaffner, SF, Freije, CA, Winnicki, S, West, K, Qu, J, Baniecki, ML, Gladden-Young, A, Lin, AE, Christopher, T-T, Ye, SH, Park, DJ, Luo, C, Barnes, KG, Shah, RR, Chak, B, Barbosa-Lima, G, Delatorre, E, Vieira, YR, Paul, LM, Tan, AL, Barcellona, CM, Porcelli, MC, Vasquez, C, Cannons, AC, Cone, MR, Hogan, KN, Kopp IV, EW, Anzinger, JJ, Garcia, KF, Parhap, LA, Gelvez Ramirez, RM, Montoya, M, Rojas, DP, Brown, CM, Hennigan, S, Sabina, B, Scotland, S, Gangavarapu, K, Grubaugh, ND, Oliveira, G, Robles-Sikisaka, R, Rambaut, A, Gehrke, L, Smole, S, Halloran, ME, Villar Centeno, LA, Mattar, S, Lorenzana, I, Cerbino-Neto, J, Valim, C, Degrave, W, Bozza, PT, Souza, TML, Bosch, I, Yozwiak, NL, MacInnis, BL & Sabeti, PC 2017, 'Genome sequencing reveals Zika virus diversity and spread in the Americas', Nature, vol. 546, pp. 411–415. https://doi.org/10.1038/nature22402

TY - JOUR

T1 - Genome sequencing reveals Zika virus diversity and spread in the Americas

AU - Metsky, Hayden C

AU - Matranga, Christian B

AU - Wohl, Shirlee

AU - Schaffner, Stephen F.

AU - Freije, Catherine A

AU - Winnicki, Sarah

AU - West, Kendra

AU - Qu, J

AU - Baniecki, Mary Lynn

AU - Gladden-Young, Adrianne

AU - Lin, Aaron E.

AU - Christopher, Tomkins-Tinch

AU - Ye, S.H

AU - Park, Daniel J

AU - Luo, Cynthia

AU - Barnes, Kayla G

AU - Shah, R.R.

AU - Chak, Bridget

AU - Barbosa-Lima, G.

AU - Delatorre, E.

AU - Vieira, Y.R.

AU - Paul, Lauren M

AU - Tan, Amanda L

AU - Barcellona, Carolyn M

AU - Porcelli, Mario C

AU - Vasquez, Chalmers

AU - Cannons, Andrew C

AU - Cone, Marshall R

AU - Hogan, Kelly N

AU - Kopp IV, Edgar W

AU - Anzinger, J.J.

AU - Garcia, K.F.

AU - Parhap, L.A.

AU - Gelvez Ramirez, R.M.

AU - Montoya, Miranda

AU - Rojas, D.P.

AU - Brown, C.M.

AU - Hennigan, S.

AU - Sabina, B.

AU - Scotland, S.

AU - Gangavarapu, K.

AU - Grubaugh, N.D.

AU - Oliveira, G.

AU - Robles-Sikisaka, R.

AU - Rambaut, Andrew

AU - Gehrke, L.

AU - Smole, S.

AU - Halloran, M.E.

AU - Villar Centeno, L.A.

AU - Mattar, S.

AU - Lorenzana, I.

AU - Cerbino-Neto, J.

AU - Valim, C.

AU - Degrave, W.

AU - Bozza, P.T.

AU - Souza, T.M.L.

AU - Bosch, I.

AU - Yozwiak, N.L.

AU - MacInnis, B.L.

AU - Sabeti, P.C.

PY - 2017/5/24

Y1 - 2017/5/24

N2 - Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

AB - Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects1,2, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analyzed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of viral surveillance. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those potentially relevant to the effectiveness of diagnostic tests.

U2 - 10.1038/nature22402

DO - 10.1038/nature22402

M3 - Article

SN - 0028-0836

VL - 546

SP - 411

EP - 415

JO - Nature

JF - Nature

ER -

Genome sequencing reveals Zika virus diversity and spread in the Americas

Abstract

Access to Document

Fingerprint

Projects

COMPARE: COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe

PREDEMICS:Preparedness,Prediction and Prevention of Emerging Zoonotic Viruses with Pandemic Potential using Multidiscipliinary Approach

Activities

NIH, Div Int Epidemiol & Populat Studies, Fogarty Int Ctr (External organisation)

Cite this