Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic

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. [Display omitted] [Display omitted] •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 A combination of travel surveillance and clinical virus genomic sequencing of infected travelers provides a framework for detecting hidden outbreaks, such as an unreported Zika outbreak in Cuba during 2017.