Metsky, Hayden CMatranga, Christian BWohl, ShirleeSchaffner, StephenFreije, CatherineWinnicki, SarahWest, Kendra L.Qu, JamesBaniecki, MaryGladden-Young, AdrianneLin, AaronTomkins-Tinch, ChristopherYe, Simon HPark, DanielLuo, CynthiaBarnes, KayleShah, RickeyChak, BridgetBarbosa-Lima, GiselleDelatorre, EdsonVieira, Yasmine RPaul, Lauren MTan, Amanda LBarcellona, Carolyn MPorcelli, Mario CVasquez, ChalmersCannons, Andrew CCone, Marshall RHogan, Kelly NKopp, Edgar WAnzinger, Joshua JGarcia, Kimberly FParham, Leda AGelvez Ramirez, Rosa MargaritaMiranda Montoya, Maria ConsueloRojas, Diana PBrown, Catherine MHennigan, ScottSabina, BrandonScotland, SarahGangavarapu, KarthikGrubaugh, Nathan DOliveira, GlennRobles-Sikisaka, RefugioRambaut, AndrewGehrke, LeeSmole, SandraHalloran, M ElizabethVillar Centeno, Luis AngelMattar, SalimLorenzana, IvetteCerbino-Neto, JoseValim, ClarissaDegrave, WimBozza, Patricia TGnirke, AndreasAndersen, Kristian GIsern, SharonMichael, ScottBozza, Fernando ASouza, Thiago MLBosch, IreneYozwiak, Nathan LMacInnis, Bronwyn LSabeti, Pardis2021-05-262017Metsky, Hayden C, Christian B. Matranga, Shirlee Wohl, Stephen Schaffner, Catherine Freije, et al. 2017. "Zika virus evolution and spread in the Americas." Nature 546: 411–415. doi: 10.1038/nature22402.https://nrs.harvard.edu/URN-3:HUL.INSTREPOS:37367721Despite 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 Brazil, 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.en-USZikaJournal Article2017-04-2620172021-05-2610.1101/109348