Date of Award

2024

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Cellular, Molecular and Biomedical Sciences

First Advisor

Emily A. Bruce

Second Advisor

Dimitry N. Krementsov

Abstract

Severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) is the pathogen responsible the pandemic beginning in 2019 that has infected 776 million people to date. This virus caused millions of deaths globally in addition to substantial socioeconomic burden and is the causative agent of coronavirus disease 19 (COVID-19). Throughout the course of the pandemic, rapid evolution of SARS-CoV-2 has allowed for the emergence of novel variants with varying virological properties. These characteristics have included increased host immune evasion, higher viral loads, and better transmission between individuals. Utilizing the characteristics of naturally emerging SARS-CoV-2 variants, we investigated different aspects which influence the transmission of this virus.

When considering the requirements for a successful human pathogen, there are several aspects to consider. From an ecological perspective, understanding the evolution and novel reservoirs of a pathogen is important to mitigate spill over risk. Our survey of hundreds of wildlife specimens native to the state of Vermont showed that none of the animals had active SARS-CoV-2 infections at the time of collection during the 2021-2022 season. However, it is important that surveillance efforts continue for various animal species to capture the emergence and progression of disease over time, especially as the variants circulating in wildlife can be antigenically different from those found in people. When considering human-to-human transmission, the evolution of the virus is also important. We showed that the viral load, or number of infectious units, was variable between different SARS-CoV-2 variants of concern (VOCs). Notably, the Delta variant, had higher viral loads than previously circulating variants, Alpha and Epsilon, perhaps contributing to its increased pathogenicity. At the molecular level, individual mutations within the genome can enhance viral replication and overall fitness. We identified a mutation within the nucleocapsid protein which allows for a novel disulfide bond to form. This bond allows for stronger nucleocapsid self-association, leading to enhanced encapsidation of viral RNA and improved fitness in vitro and in vivo. Further studies will continue to elucidate the connection between this novel cystine and improved fitness of the viral lifecycle.

Characterization of these cellular mechanics could identify novel pharmacological targets or improved vaccines. When applied, these results could help alleviate some of the burden of SARS-CoV-2 or future emergent CoVs. Understanding the evolution of the virus within reservoir species will allow for spill over risk-reduction and better protection of agricultural workers. Knowing the different properties between variants that emerged, while a retrospective analysis, helps us learn which measures to investigate in the future to make better informed health decisions for the public. Lastly, understanding the molecular mechanisms of the virus allows for better therapeutics to be created and ultimately helps reduce the burden of this now endemic virus. Comprehensive knowledge of a pathogen at a spectrum spanning macro to microscopic scale allows for robust public health decisions to be made that both help prevent future outbreaks and mitigate the damage currently being experienced.

Language

en

Number of Pages

230 p.

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