Zika virus evolution and spread in the Americas

Metsky, Hayden C., Matranga, Christian B., Wohl, Shirlee, Schaffner, Stephen F., Freije, Catherine A., Winnicki, Sarah M., West, Kendra, Qu, James, Baniecki, Mary Lynn, Gladden-Young, Adrianne, Lin, Aaron E., Tomkins-Tinch, Christopher H., Ye, Simon H., Park, Daniel J., Luo, Cynthia Y., Barnes, Kayla G., Shah, Rickey R., Chak, Bridget, Barbosa-Lima, Giselle, Delatorre, Edson, Vieira, Yasmine R., Paul, Lauren M., Tan, Amanda L., Barcellona, Carolyn M., Porcelli, Mario C., Vasquez, Chalmers, Cannons, Andrew C., Cone, Marshall R., Hogan, Kelly N., Kopp, Edgar W., Anzinger, Joshua J., Garcia, Kimberly F., Parham, Leda A., Ramírez, Rosa M.Gélvez, Montoya, Maria C.Miranda, Rojas, Diana P., Brown, Catherine M., Hennigan, Scott, Sabina, Brandon, Scotland, Sarah, Gangavarapu, Karthik, Grubaugh, Nathan D., Oliveira, Glenn, Robles-Sikisaka, Refugio, Rambaut, Andrew, Gehrke, Lee, Smole, Sandra, Halloran, M. Elizabeth, Villar, Luis, Mattar, Salim, Lorenzana, Ivette, Cerbino-Neto, Jose, Valim, Clarissa, Degrave, Wim, Bozza, Patricia T., Gnirke, Andreas, Andersen, Kristian G., Isern, Sharon, Michael, Scott F., Bozza, Fernando A., Souza, Thiago M.L., Bosch, Irene, Yozwiak, Nathan L., Macinnis, Bronwyn L., and Sabeti, Pardis C. (2017) Zika virus evolution and spread in the Americas. Nature, 546. pp. 411-415.

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Abstract

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using 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 analysed 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 United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.

Item ID: 60729
Item Type: Article (Research - C1)
ISSN: 1476-4687
Keywords: Zika virus, evolution, spread,outbreak, phylodynamics
Copyright Information: © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.
Additional Information:

Funding was provided by: Marc and Lynne Benioff (P.C.S.); NIH NIAID U19AI110818 (Broad Institute); Howard Hughes Medical Institute (P.C.S.); Harvard University Burke Global Health Fellowship (P.C.S.); Broad Institute BroadNext10 program (A.G. and P.C.S.); AWS Cloud Credits for Research (P.C.S.); Conselho Nacional de Desenvolvimento Científico e Tecnológico (440909/2016-3) and Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro (E-26/201.320/2016, E-26/201.332/2016, E-26/010.000194/2015) (P.T.B. and F.A.B.); NIH NIAID 1R01AI099210 (S.I. and S.F.M.); MIDAS-National Institute of General Medical Sciences U54GM111274 (M.E.H. and D.P.R.); NIH NIAID AI100190 (I.B. and L.G.); AEDES Network (I.B.) and Colombian Science, Technology and Innovation Fund of Sistema General de Regalías-BPIN 2013000100011 (L.V., R.M.G.R., M.C.M.M., and I.B.); ASTMH Shope Fellowship (K.G.B.); NSF DGE 1144152 (A.E.L.); PNPD/CAPES Postdoctoral Fellowship (E.D.); Fulbright-Colciencias Doctoral Scholarship (D.P.R.); NIH training grant 5T32AI007244-33 (N.D.G.); EU under grant agreements 278433-PREDEMICS and 643476-COMPARE (A.R.); and NIH NCATS CTSA UL1TR001114, NIH NIAID contract HHSN272201400048C, The Ray Thomas Foundation, and Pew Biomedical Scholarship (K.G.A.).

Date Deposited: 30 Oct 2019 02:09
FoR Codes: 06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060309 Phylogeny and Comparative Analysis @ 50%
11 MEDICAL AND HEALTH SCIENCES > 1117 Public Health and Health Services > 111706 Epidemiology @ 25%
11 MEDICAL AND HEALTH SCIENCES > 1103 Clinical Sciences > 110309 Infectious Diseases @ 25%
SEO Codes: 92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920404 Disease Distribution and Transmission (incl. Surveillance and Response) @ 100%
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