TY - JOUR T1 - Genome sequencing reveals Zika virus diversity and spread in the Americas JF - bioRxiv DO - 10.1101/109348 SP - 109348 AU - H.C. Metsky AU - C.B. Matranga AU - S. Wohl AU - S.F. Schaner AU - C.A. Freije AU - S. M. Winnicki AU - K. West AU - J. Qu AU - M.L. Baniecki AU - A. Gladden-Young AU - A.E. Lin AU - C.H. Tomkins-Tinch AU - D.J. Park AU - C.Y. Luo AU - K.G. Barnes AU - B. Chak AU - G. Barbosa-Lima AU - E. Delatorre AU - Y.R. Vieira AU - L.M. Paul AU - A.L. Tan AU - M.C. Porcelli AU - C. Vasquez AU - A.C. Cannons AU - M.R. Cone AU - K.N. Hogan AU - E.W. Kopp IV AU - J.J. Anzinger AU - K.F. Garcia AU - L.A. Parham AU - R.M. Gélvez Ramírez AU - M.C. Miranda Montoya AU - D.P. Rojas AU - C.M. Brown AU - S. Hennigan AU - B. Sabina AU - S. Scotland AU - K. Gangavarapu AU - N.D. Grubaugh AU - G. Oliveira AU - R. Robles-Sikisaka AU - A. Rambaut AU - L. Gehrke AU - S. Smole AU - M.E. Halloran AU - L.A. Villar Centeno AU - S. Mattar AU - I. Lorenzana AU - J. Cerbino-Neto AU - W. Degrave AU - P.T. Bozza AU - A. Gnirke AU - K.G. Andersen AU - S. Isern AU - S. Michael AU - F. Bozza AU - T.M.L. Souza AU - I. Bosch AU - N.L. Yozwiak AU - B.L. MacInnis AU - P.C. Sabeti Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/02/18/109348.abstract N2 - Despite great attention given to the recent Zika virus (ZIKV) epidemic in the Americas, much remains unknown about its epidemiology and evolution, in part due to a lack of genomic data. We applied multiple sequencing approaches to generate 100 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, confirming phylogenetic evidence for the origin and rapid expansion of the outbreak in Brazil1, and for multiple introductions from Brazil into Honduras, Colombia, Puerto Rico, other Caribbean islands, and the continental US. We find that ZIKV circulated undetected in many regions of the Americas for up to a year before the first locally transmitted cases were confirmed, highlighting the challenge of effective surveillance for this virus. We further characterize genetic variation across the outbreak to identify mutations with possible functional implications for ZIKV biology and pathogenesis. ER -