Date of Award

January 2023

Document Type

Open Access Thesis

Degree Name

Master of Public Health (MPH)


School of Public Health

First Advisor

Nathan Grubaugh

Second Advisor

Theodore Cohen


The ongoing SARS-CoV-2 pandemic is marked by continuing emergence of novel Omicron variants. However, the mechanism with which these lineages establish themselves in new geographical areas remains an understudied subject. In this research, we utilized a discrete phylogeographical analysis framework on 19,608 SARS-CoV-2 sequences of the BA.5 Omicron lineages between February and June 2022, in order to better understand how the variant emerged in different regions of the United States. We found that the earliest BA.5 introductions came from Africa, befitting the origin of the lineage. Additionally, we discovered extensive domestic transmission between the Department of Health and Human Services (HHS) regions of America through both neighboring effects and cross-country transmission. We found further evidence that two key regions that include California and Florida drove most within-U.S. introduction events of BA.5. Our results suggest a pattern of foreign importation and domestic spread, through interaction of these hotspot areas, and form a framework for understanding novel variant emergence in the United States.


This is an Open Access Thesis.

Open Access

This Article is Open Access