Abstract
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.
Highlights
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
At least 8 separate foreign-introduction events were captured within the ancestry of the viruses sequenced, including 2 that expanded into autochthonous lineages and 6 separate introduction events represented by individual sequences associated with genomes from the United States, the Caribbean, South America, and Central America, suggesting limited spread
Bayesian reconstruction of Puerto Rico clade 1 (PR C1) presents the largest autochthonous monophyletic cluster that originated from viruses from South America and the Caribbean, including Brazil, Suriname, French Guyana, the US Virgin Islands, and Dominican Republic (Figure). tMRCA estimates place the divergence of PR C1 in mid-June 2015 (95% highest posterior density [HPD] February 2015–October 2015) and a within-outbreak evolutionary rate of 1.61 × 10−3 (95% HPD 1.13–2.10 × 10−3) substitutions/site/year
Summary
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. Puerto Rico reported the first confirmed case of Zika virus (ZIKV) disease in November 2015 and subsequently experienced epidemic transmission that peaked by mid-August 2016 [1].
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