PT - JOURNAL ARTICLE AU - N. R. Faria AU - J. Quick AU - I. Morales AU - J. Thézé AU - J.G. Jesus AU - M. Giovanetti AU - M. U. G. Kraemer AU - S. C. Hill AU - A. Black AU - A. C. da Costa AU - L.C. Franco AU - S. P. Silva AU - C.-H. Wu AU - J. Ragwhani AU - S. Cauchemez AU - L. du Plessis AU - M. P. Verotti AU - W. K. de Oliveira AU - E. H. Carmo AU - G. E. Coelho AU - A. C. F. S. Santelli AU - L. C. Vinhal AU - C. M. Henriques AU - J. T. Simpson AU - M. Loose AU - K. G. Andersen AU - N. D. Grubaugh AU - S. Somasekar AU - C. Y. Chiu AU - L. L. Lewis-Ximenez AU - S.A. Baylis AU - A. O. Chieppe AU - S. F. Aguiar AU - C. A. Fernandes AU - P. S. Lemos AU - B. L. S. Nascimento AU - H. A. O. Monteiro AU - I. C. Siqueira AU - M. G. de Queiroz AU - T. R. de Souza AU - J. F. Bezerra AU - M. R. Lemos AU - G. F. Pereira AU - D. Loudal AU - L. C. Moura AU - R. Dhalia AU - R. F. França AU - T. Magalhães AU - E. T. Marques, Jr. AU - T. Jaenish AU - G. L. Wallau AU - M. C. de Lima AU - V. Nascimento AU - E. M. de Cerqueira AU - M. M. de Lima AU - D. L. Mascarenhas AU - J. P. Moura Neto AU - A. S. Levin AU - T. R. Tozetto-Mendoza AU - S. N. Fonseca AU - M. C. Mendes-Correa AU - F.P. Milagres AU - A. Segurado AU - E. C. Holmes AU - A. Rambaut AU - T. Bedford AU - M. R. T. Nunes AU - E. C. Sabino AU - L. C. J. Alcantara AU - N. Loman AU - O. G. Pybus TI - Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas AID - 10.1101/105171 DP - 2017 Jan 01 TA - bioRxiv PG - 105171 4099 - http://biorxiv.org/content/early/2017/02/03/105171.short 4100 - http://biorxiv.org/content/early/2017/02/03/105171.full AB - Zika virus (ZIKV) transmission in the Americas was first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (>200,000 by 24 Dec 20162) as well as the greatest number of cases associated with microcephaly and other birth defects (2,366 confirmed cases by 31 Dec 20162). Following the initial detection of ZIKV in Brazil, 47 countries and territories in the Americas have reported local ZIKV transmission, with 22 of these reporting ZIKV-associated severe disease3. Yet the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of such information for interpreting past trends in reported microcephaly. To address this we generated 53 complete or partial ZIKV genomes, mostly from Brazil, including data generated by the ZiBRA project – a mobile genomics lab that travelled across Northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Joint analyses of viral genomes with ecological and epidemiological data estimate that the ZIKV epidemic first became established in NE Brazil by March 2014 and likely disseminated from there, both nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil coincide with periods of high vector suitability in recipient regions and indicate the duration of pre-detection cryptic transmission in those regions. NE Brazil’s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus’ basic reproduction number.One Sentence Summary Virus genomes reveal the establishment of Zika virus in Northeast Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.