PT - JOURNAL ARTICLE AU - H.C., Metsky AU - C.B., Matranga AU - S., Wohl AU - S.F., Schaffner 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 - S.H., Ye AU - D.J., Park AU - C.Y., Luo AU - K.G., Barnes AU - R.R., Shah AU - B., Chak AU - G., Barbosa-Lima AU - E., Delatorre AU - Y.R., Vieira AU - L.M., Paul AU - A.L., Tan AU - C.M., Barcellona AU - M.C., Porcelli AU - C., Vasquez AU - A.C., Cannons AU - M.R., Cone AU - K.N., Hogan AU - E.W., Kopp 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 - C., Valim AU - W., Degrave AU - P.T., Bozza AU - A., Gnirke AU - K.G., Andersen AU - S., Isern AU - S.F., Michael AU - F.A., Bozza AU - T.M.L., Souza AU - I., Bosch AU - N.L., Yozwiak AU - B.L., MacInnis AU - P.C., Sabeti TI - Genome sequencing reveals Zika virus diversity and spread in the Americas AID - 10.1101/109348 DP - 2017 Jan 01 TA - bioRxiv PG - 109348 4099 - http://biorxiv.org/content/early/2017/04/23/109348.short 4100 - http://biorxiv.org/content/early/2017/04/23/109348.full AB - 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.