@article {H.C.109348, author = {Metsky H.C. and Matranga C.B. and Wohl S. and Schaffner S.F. and Freije C.A. and Winnicki S.M. and West K. and Qu J. and Baniecki M.L. and Gladden-Young A. and Lin A.E. and Tomkins-Tinch C.H. and Ye S.H. and Park D.J. and Luo C.Y. and Barnes K.G. and Shah R.R. and Chak B. and Barbosa-Lima G. and Delatorre E. and Vieira Y.R. and Paul L.M. and Tan A.L. and Barcellona C.M. and Porcelli M.C. and Vasquez C. and Cannons A.C. and Cone M.R. and Hogan K.N. and Kopp E.W. and Anzinger J.J. and Garcia K.F. and Parham L.A. and G{\'e}lvez Ram{\'\i}rez R.M. and Miranda Montoya M.C. and Rojas D.P. and Brown C.M. and Hennigan S. and Sabina B. and Scotland S. and Gangavarapu K. and Grubaugh N.D. and Oliveira G. and Robles-Sikisaka R. and Rambaut A. and Gehrke L. and Smole S. and Halloran M.E. and Villar Centeno L.A. and Mattar S. and Lorenzana I. and Cerbino-Neto J. and Valim C. and Degrave W. and Bozza P.T. and Gnirke A. and Andersen K.G. and Isern S. and Michael S.F. and Bozza F.A. and Souza T.M.L. and Bosch I. and Yozwiak N.L. and MacInnis B.L. and Sabeti P.C.}, 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 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.}, URL = {https://www.biorxiv.org/content/early/2017/04/23/109348}, eprint = {https://www.biorxiv.org/content/early/2017/04/23/109348.full.pdf}, journal = {bioRxiv} }