@article {Metsky109348, author = {H.C. Metsky and C.B. Matranga and S. Wohl and S.F. Schaner and C.A. Freije and S. M. Winnicki and K. West and J. Qu and M.L. Baniecki and A. Gladden-Young and A.E. Lin and C.H. Tomkins-Tinch and D.J. Park and C.Y. Luo and K.G. Barnes and B. Chak and G. Barbosa-Lima and E. Delatorre and Y.R. Vieira and L.M. Paul and A.L. Tan and M.C. Porcelli and C. Vasquez and A.C. Cannons and M.R. Cone and K.N. Hogan and E.W. Kopp IV and J.J. Anzinger and K.F. Garcia and L.A. Parham and R.M. G{\'e}lvez Ram{\'\i}rez and M.C. 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 A. Rambaut and L. Gehrke and S. Smole and M.E. Halloran and L.A. Villar Centeno and S. Mattar and I. Lorenzana and J. Cerbino-Neto and W. Degrave and P.T. Bozza and A. Gnirke and K.G. Andersen and S. Isern and S. Michael and F. Bozza and T.M.L. Souza and I. Bosch and N.L. Yozwiak and B.L. MacInnis and P.C. Sabeti}, title = {Genome sequencing reveals Zika virus diversity and spread in the Americas}, elocation-id = {109348}, year = {2017}, doi = {10.1101/109348}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2017/02/18/109348}, eprint = {https://www.biorxiv.org/content/early/2017/02/18/109348.full.pdf}, journal = {bioRxiv} }