Honors Program


Date of this Version


Document Type



Hart, Kaitlyn. Elucidation of Transmission Pathways of SARS-CoV-2 between Human and Non-Human Animal Populations. Undergraduate Honors Thesis, University of Nebraska-Lincoln, 2024.


Copyright Kaitlyn Hart 2024


The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus behind the global novel coronavirus disease 2019 (COVID-19) pandemic. The continuous emergence and evolution of new variants of SARS-CoV-2 has complicated the handling and prevention of the COVID-19 pandemic. Animal populations can become viral reservoirs where individual animals are susceptible to the virus but remain asymptomatic upon infection, allowing mutations to accumulate in the viral genome. The goal of our research is to understand how SARS-CoV-2 has been moving through the Nebraska populations and to identify possible viral reservoirs that are important for the public health concerns in Nebraska. The objectives in this study were to build a database of SARS-CoV-2 genomes especially focusing on those collected from humans in Nebraska as well as non-human hosts, perform phylogenetic analysis of these genomes, and elucidate the transmission pathways of SARS-CoV-2 between human and non-human hosts in Nebraska. A total of 35,129 SARS-CoV-2 genomic sequences were gathered from humans in Nebraska. SARS-CoV-2 genomic sequences were also collected from fifty non-human hosts, totaling 3,232 sequences. Our phylogenetic analysis confirmed that SARS-CoV-2 sequences have high sequence similarities within the same variants and more diversity between different variants, regardless of sampling location or host organism from which the virus was obtained. The phylogenetic analysis also gave some insight into possible transmission pathways of SARSCoV-2 between human and non-human hosts. The genomes collected in this study were compiled into a database that will be useful for future studies on SARS-CoV-2 transmission pathways not only in Nebraska but also worldwide.