Date of Award

January 2022

Document Type


Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Nathan D. Grubaugh


Pathogen genomic surveillance systems have proven invaluable throughout the course of the global COVID-19 pandemic. Despite this, genomic surveillance programs are under-resourced or nonexistent in regions with reduced access to advanced public health tools, like the Caribbean. In this study, we documented and evaluated the establishment of a genomic surveillance system in the U.S. Virgin Islands during 2021, and used data from the program to place the story of COVID-19 in the U.S. Virgin Islands in a global context. We constructed a phylogenetic tree and conducted phylogeographic analyses to estimate the timing and geographic origin of the most recent common ancestor of each introduction to the U.S. Virgin Islands. Our tree estimated that the number of introductions peaks in January 2021, with a smaller peak during June. The origins of these hypothesized introductions are diverse; nearly every region of the world is represented, though North America, Europe, and Africa contribute the largest share of estimated introductions. To better assess the impact of travelers into the territory, we also constructed a statistical model using global COVID-19 case numbers, SARS-CoV-2 variant frequencies, and international air travel volume to estimate the number and origin of variant introductions into the U.S. Virgin Islands during 2021. Our model estimated that introductions of SARS-CoV-2 peaked in August 2021, approximately the same time that cases in the U.S. Virgin Islands reached their peak. Our model also projected that nearly all introductions came from North America. The contrast between our tree and our statistical model highlights issues with relying on phylogeographic analyses during a pandemic, while also demonstrating the necessity of considering inbound travel volume in a region whose economy relies heavily on tourism.


This thesis is restricted to Yale network users only. It will be made publicly available on 05/19/2024