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GeoSentinel Surveillance Network Keywords genomic epidemiology; infectious disease genomics; clinical sequencing; travel surveillance; Zika virus; phylogenetics; virus sequencing; Zika epidemic Highlights * Travel surveillance and genomics uncovered hidden Zika transmission * An unreported and 1-year delayed Zika outbreak was detected in Cuba * Mosquito control may delay, not prevent, Zika virus establishment * A surveillance framework to detect hidden outbreaks was created Summary The Zika epidemic in the Americas has challenged surveillance and control. As the epidemic appears to be waning, it is unclear whether transmission is still ongoing, which is exacerbated by discrepancies in reporting. To uncover locations with lingering outbreaks, we investigated travel-associated Zika cases to identify transmission not captured by reporting. We uncovered an unreported outbreak in Cuba during 2017, a year after peak transmission in neighboring islands. By sequencing Zika virus, we show that the establishment of the virus was delayed by a year and that the ensuing outbreak was sparked by long-lived lineages of Zika virus from other Caribbean islands. Our data suggest that, although mosquito control in Cuba may initially have been effective at mitigating Zika virus transmission, such measures need to be maintained to be effective. Our study highlights how Zika virus may still be 'silently' spreading and provides a framework for understanding outbreak dynamics. Video Abstract Display Omitted Author Affiliation: (1) Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA (2) Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA (3) Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON M5B 1T8, Canada (4) Department of Biological Sciences, Florida Gulf Coast University, Fort Myers, FL 33965, USA (5) Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL 33612, USA (6) Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA (7) Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702, USA (8) Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA (9) Department of Zoology, University of Oxford, Oxford OX1 3PS, UK (10) Boston Children's Hospital, Boston, MA 02115, USA (11) Harvard Medical School, Boston, MA 02115, USA (12) Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL 32399, USA (13) Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Miami, FL 33125, USA (14) Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA (15) MassBiologics, University of Massachusetts Medical School, Boston, MA 02126, USA (16) Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA (17) Section of Infectious Diseases, Department of Medicine, Boston Medical Center, Boston, MA 02118, USA (18) School of Civil and Environmental Engineering, UNSW Sydney, Sydney, NSW 2052, Australia (19) Department of Civil Engineering, Johns Hopkins University, Baltimore, MD 21287, USA (20) Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium (21) Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON M5B 1T8, Canada (22) Scripps Research Translational Institute, La Jolla, CA 92037, USA * Corresponding author Article History: Received 19 December 2018; Revised 15 April 2019; Accepted 12 July 2019 (miscellaneous) Published: August 22, 2019 (footnote)23 These authors contributed equally (footnote)24 Senior author (footnote)25 Lead Contact Byline: Nathan D. Grubaugh [nathan.grubaugh@yale.edu] (1,2,23,*), Sharada Saraf (2,23), Karthik Gangavarapu (2,23), Alexander Watts (3), Amanda L. Tan (4,5), Rachel J. Oidtman (6), Jason T. Ladner (7,8), Glenn Oliveira (2), Nathaniel L. Matteson (2), Moritz U.G. Kraemer (9,10,11), Chantal B.F. Vogels (1), Aaron Hentoff (1), Deepit Bhatia (3), Danielle Stanek (12), Blake Scott (12), Vanessa Landis (12), Ian Stryker (5), Marshall R. Cone (5), Edgar W. Kopp IV (5), Andrew C. Cannons (5), Lea Heberlein-Larson (5), Stephen White (13), Leah D. Gillis (13), Michael J. Ricciardi (14), Jaclyn Kwal (14), Paola K. Lichtenberger (14), Diogo M. Magnani (14,15), David I. Watkins (14), Gustavo Palacios (7), Davidson H. Hamer (16,17), Lauren M. Gardner (18,19), T. Alex Perkins (6), Guy Baele (20), Kamran Khan (3,21), Andrea Morrison (12,24), Sharon Isern (4,24), Scott F. Michael [smichael@fgcu.edu] (4,24,**), Kristian G. Andersen [andersen@scripps.edu] (2,22,24,25,***)