Hayden C. Metsky, Christian B. Matranga, Shirlee Wohl, Stephen F. Schaffner, Catherine A. Freije, Sarah M. Winnicki, Kendra West, James Qu, Mary Lynn Baniecki, Adrianne Gladden-Young, Aaron E. Lin, Christopher H. Tomkins-Tinch, Simon H. Ye, Daniel J. Park, Cynthia Y. Luo, Kayla G. Barnes, Rickey R. Shah, Bridget Chak, Giselle Barbosa-Lima, Edson Delatorre, Yasmine R. Vieira, Lauren M. Paul, Amanda L. Tan, Carolyn M. Barcellona, Mario C. Porcelli, Chalmers Vasquez, Andrew C. Cannons, Marshall R. Cone, Kelly N. Hogan, Edgar W. Kopp, Joshua J. Anzinger, Kimberly F. Garcia, Leda A. Parham, Rosa M. Gélvez Ramírez, Maria C. Miranda Montoya, Diana P. Rojas, Catherine M. Brown, Scott Hennigan, Brandon Sabina, Sarah Scotland, Karthik Gangavarapu, Nathan D. Grubaugh, Glenn Oliveira, Refugio Robles-Sikisaka, Andrew Rambaut, Lee Gehrke, Sandra Smole, M. Elizabeth Halloran, Luis Villar, Salim Mattar, Ivette Lorenzana, Jose Cerbino-Neto, Clarissa Valim, Wim Degrave, Patricia T. Bozza, Andreas Gnirke, Kristian G. Andersen, Sharon Isern, Scott F. Michael, Fernando A. Bozza, Thiago M. L. Souza, Irene Bosch, Nathan L. Yozwiak, Bronwyn L. MacInnis, Pardis C. Sabeti
May 24, 2017
Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using 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 analysed 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 United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests.