Date of Award

January 2020

Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Nathan D. Grubaugh


During the larger epidemic in the Americas, Puerto Rico experienced an epidemic of Zika virus (ZIKV) between November 2015 and December 2016. During this period, 39,717 residents tested positive, or 1.1% of the population. Our team sequenced 84 ZIKV genomes directly from archived ZIKV-positive clinical samples from throughout the epidemic period, and from distinct regions of the island, in order to reconstruct the introduction(s) to and geographic spread of ZIKV in Puerto Rico. We found that ZIKV was circulating in the Greater Antilles by April (95% CI: February-June) of 2015, and was introduced to Puerto Rico by August (95% CI: July-November) of 2015. While there were multiple introductions, just two showed evidence of sustained transmission and just one lineage included 77% of the samples in our data set. Coastal areas of the island, particularly the northeastern coast, saw early introductions and were sources of introductions to other areas of the island. Spread was highly correlated with ZIKV incidence at the origin, and not with volume of travel between locations. This epidemic is part of a growing trend of increasing arbovirus emergence and burden in the Americas and the Caribbean in particular, underscoring the importance of understanding dynamics specific to Puerto Rico as well as general driving factors behind epidemic and endemic arbovirus spread.


This is an Open Access Thesis.

Open Access

This Article is Open Access