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.