We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.
Keywords: NGS; Puerto Rico; United States; Zika; Zika virus; genomic epidemiology; molecular evolution; next-generation sequencing; phylogenetics; vector-borne infections; viruses.