Virology Commons^™

An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield

Masters Theses

Herpesviruses persist as a parasitic actor among many species. These viral agents can rapidly seize control over host cells by influencing global gene expression. Through a process known as host shutoff, herpesviruses cause a widespread degradation event of host transcripts within the cytoplasm. Specifically, Kaposi Sarcoma associated herpesvirus (KSHV) encodes for an endoribonuclease, termed SOX, that orchestrates this manipulation of gene expression. We and others have discovered certain transcripts that escape this fate; we suggest that this is an active escape, where transcripts have 3’ UTR elements that disallow SOX cleavage. One of the escapees that has been found is …

Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro

Doctoral Dissertations

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …

Developing Disinfection Strategies For Controlling Human Norovirus, Sars-Cov-2, And Clostridioides Difficile Endospores In Long-Term Care Facilities, Jinge Huang

All Dissertations

Long-term care facilities (LTCFs) provide an environment favorable for the transmission of three critical human pathogens: human norovirus (HuNoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Clostridioides difficile. Given residents in LTCFs are susceptible to infections due to their advanced ages and compromised immune systems, effective environmental surface disinfection plays a crucial role in controlling the spread of human pathogens within these settings and, therefore, mitigates the risk of infections caused by these pathogens. This dissertation aimed to assess the efficacy of various types of disinfectants against two HuNoV surrogates [feline calicivirus (FCV) and Tulane virus (TuV)], two …

Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi

Doctoral Dissertations

Viruses, owing to their ubiquitous nature and ability to infect almost every other species, have long been a subject of interest for scientists. Some of the virus species can be very deadly to humans and animals alike and can impose a huge economic and health burden across the world. The recent CoVID-19 pandemic underscores the importance of timely detection for developing effective intervention strategies. Unfortunately, some of the virus species that cause significant health and economic impacts do not have robust and reliable detection methods due to several reasons. In some cases, despite having gold standard methods for detection of …

Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker

Masters Theses

Viruses hold our attention for the horrific impact they have on human health and welfare. However, viruses are a critical part of our ecosystem and facilitate the cycling of carbon and other important nutrients. The cycle of virus infection, followed by host resistance and the subsequent evolution of new strains enables adaptation to changing hosts and the environment. Giant viruses, some with particle sizes large enough to be visible in light microscopes and their bewildering array of accessory genes, have captivated scientists and the general public since their discovery two decades ago. Giant viruses are part of the Nucleocytoviricota (NCV) …

Functional Characterization Of The Human And Murine Schlafen Family Group Iii, Carlos A. Valenzuela

Open Access Theses & Dissertations

The Schlafen (SLFN) family of proteins are known for being encoded by interferon stimulated genes. The family is divided into three groups (I, II, III), for which the largest in size belong to the subgroup III. In humans, group III has the most members (SLFN5, SLFN11, SLFN13 and SLFN14); there is no member of group I and only one member of group II (SLFN12). All human SLFNs belonging to group III have been reported to impair viral protein expression or infection across a variety of viruses. The antiviral function is mediated in SLFN11 and SLFN13 by their tRNase activity, and …

Evolution Of Overlapping Reading Frames In Virus Genomes, Laura Muñoz Baena

Electronic Thesis and Dissertation Repository

Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones.

To characterize …

Analyzing Pseudomonas Aeruginosa With Bacteriophage Tags Using Photoacoustic Flow Cytometry, Jennifer C. Schinke

Electronic Theses and Dissertations

The number of daily bacterial infections is climbing and the CDC explains that this is due to the antibiotic-resistant threat in the United States. Finding a faster way of bacterial identification is necessary as it currently takes 1-4 days for a medical lab to culture and identify bacteria. Photoacoustic flow cytometry (PAFC) can be used as an alternative method resulting in swift identification within an hour (Edgar, 2019). Pseudomonas aeruginosa, cell line PA01, will be coated in up to a few hundred red dyed phages making it detectible by the photoacoustic flow cytometry system. Bacteriophages (phages) are viruses that …

A Shift In Rna Fate: Investigating The Role Of C19orf66 During Kshv Lytic Replication, William Rodriguez Jr.

Doctoral Dissertations

During viral infection, virus and host clash for control of the cell in a conflict that ultimately drives the evolution of both sides and has lasting consequences in the form of pathogenesis. At the heart of this struggle is a contest for control of cellular gene expression, a struggle epitomized by an evolutionary tug-of-war for supremacy over RNA fate. During lytic replication, Kaposi’s sarcoma-associated herpesvirus (KSHV) triggers a massive RNA decay event known as viral “Host Shutoff” which decimates greater than 70% of the host transcriptome, simultaneously suppressing the cellular anti-viral response and freeing host resources for viral replication. However, …

Vertical Transmission Of Zika Virus In Monodelphis Domestica, Mohini Moulick

Theses and Dissertations

Zika Viral infection in pregnant women may lead to infants born with microcephaly and other neurological complications, making Zika viral research imperative. Prior research demonstrated Monodelphis domestica to be a unique animal model for Zika virus studies, and viral proteins were detected in brain tissue of juveniles after intracerebral inoculation of infants. We wanted to determine if we can detect a viral protein, non-structural protein 1 (NS1), in brain tissue after intraperitoneal inoculation and we found it to be possible through immunohistochemistry (IHC) analysis. We also investigated if inoculated dams (mothers) would give rise to Zika positive pups (natural inoculation), …

Exploration Of The Immune Landscape Of Ebv-Associated Gastric Cancers, Mikhail Salnikov

Electronic Thesis and Dissertation Repository

Epstein–Barr virus (EBV) is a gammaherpesvirus associated with 9% of all gastric cancers (GCs). EBV-associated GCs (EBVaGCs) are pathologically and clinically distinct entities from EBV-negative GCs (EBVnGCs), with EBVaGCs exhibiting differential molecular pathology and patient prognosis. The purpose of this thesis is to investigate the tumor microenvironment (TME) of EBVaGCs, which has not been explored in-depth. We hypothesize that EBVaGCs and EBVnGCs are also distinct in terms of the molecular immune landscape. We employed over 400 stomach adenocarcinoma (STAD) samples from The Cancer Genome Atlas (TCGA), as well as a single cell dataset, for the construction of a web suite …

Development Of Recombinant Varicella-Zoster Virus Vaccines Expressing Sars-Cov-2 Antigens, Cody Wilson

Honors Theses

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) continues to cause infections and deaths around the globe. Since its emergence, scientists have worked diligently to discover and produce vaccines to battle the virus. While they successfully created and distributed vaccines, the vaccines are not without flaw. These vaccines do not grant long term immunity, require multiple booster shots, and have not prevented the emergence of viral variants. In this study, the SARS-CoV-2 receptor binding domain (RBD), which is a key part of the spike protein (S), and nucleocapsid (N) genetic sequences were inserted into the live varicella …

An Ecological Perspective Of American Rodent-Borne Orthohantavirus Surveillance, Nathaniel Mull

Graduate Theses and Dissertations

Orthohantaviruses are a global group of viruses found primarily in rodents, though several viruses have also been found in shrews and moles. Many rodent-borne orthohantaviruses are capable of causing one of several diseases in humans, and the mortality associated with these diseases ranges from < 0.1% - 50% depending on the specific etiological virus. In North and South America, orthohantavirus research was ignited by an outbreak of severe disease in the Four Corners region of the United States in 1993. However, despite the discovery of over 20 orthohantaviruses in the Americas, our understanding of orthohantavirus ecology and virus-host dynamics in this region is still limited, and orthohantavirus surveillance is generally restricted in scope to select regions and small portions of host distributional ranges. In Chapter I, I present a literature review on the current understanding of American rodent-borne orthohantavirus ecology. This review focused on under-studied orthohantaviruses, addressing gaps in knowledge by extrapolating information from well-studied orthohantaviruses, general rodent ecology, and occassionally from Eurasian orthohantavirus-host ecology. There were several key conclusions generated from this review that warrant further research: 1) the large number of putative orthohantaviruses and gaps in orthohantavirus evolution necessitate further surveillance and characterization, 2) orthohantavirus traits differ and are more generalizable based on host taxonomy rather than geography, and 3) orthohantavirus host species are disproportionately found in grasslands and disturbed habitats. In Chapter II, I present a prioritized list of rodent species to target for orthohantavirus surveillance based on predictive modeling using machine learning. Probable orthohantavirus hosts were predicted based on traits of known orthohantavirus hosts using two different types of evidence: RT-PCR and virus isolation. Predicted host distributions were also mapped to identify geographic hotspots to spatially guide future surveillance efforts. In Chapter III, I present a framework for understanding and predicting orthohantavirus traits based on reservoir host phylogeny, as opposed to the traditional geographic dichotomy used to group orthohantaviruses. This framework establishes three distinct orthohantavirus groups: murid-borne orthohantaviruses, arvicoline-borne orthohantaviruses, and non-arvicoline cricetid-borne orthohantaviruses, which differ in several key traits, including the human disease they cause, transmission routes, and virus-host fidelity. In Chapter IV, I compare rodent communities and orthohantavirus prevalence among grassland management regimes. Sites that were periodically burned had high rodent diversity and a high proportion of grassland species. However, rodent seroprevalence for orthohantavirus was also highest in burned sites, representing a trade-off in habitat management outcomes. The high seroprevalence in burned sites is likely due to the robust populations supported by the high quality habitat resulting from prescribed burning. In Chapters V and VI, I describe Ozark virus and Sager Creek virus, two novel orthohantaviruses discovered from specimens collected during Chapter IV. Both chapters report full genome sequences of the respective viruses and compare both nucleotide and protein phylogenies with related orthohantaviruses. Additionally in Chapter VI, I support the genetic analyses with molecular and ecological characterizations, including seasonal fluctuations in host abundance, correlates of prevalence, evidence of virus shedding, and information on host cell susceptibility to Sager Creek virus.

The Alphaviral Capsid Protein Inhibits Irak1-Dependent Tlr Signaling To Promote Pathogenesis., V. "Trey" Landers

Electronic Theses and Dissertations

Alphaviruses are positive-sense RNA viruses spread by mosquitos. They can cause a severe multi-joint febrile arthritis or encephalitis resulting in death or life-long cognitive impairments. To date there are no approved antiviral therapeutics or vaccine strategies for the treatment of alphaviruses creating a critical need to better understand the host pathogen interactions of alphaviruses that enable pathogenesis. It is known that alphaviruses evade innate immune responses by shutting down host transcription and translation, but these methods are dependent on viral gene expression and leave a critical time frame during early infection before viral gene expression has begun that the virus …

Disinfectant Efficacy Against Sars-Cov-2 Surrogates, Bovine Coronavirus And Human Coronavirus Oc43, On Hard And Soft Non-Porous Surfaces, Breanna Kimbrell

All Theses

The novel human coronavirus (HCoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged from Wuhan, China in the latter part of 2019. The rapid spread of SARS-CoV-2 amid the most recent COVID-19 pandemic forced countless foodservice establishments (FSEs) across the United States to close, taking a tremendous toll on the foodservice industry. Although primarily transmitted person-to-person, previous studies indicate that the duration of SARS-CoV-2 survival on different environmental surfaces provides adequate time for secondary transmission to occur. To prevent the further spread of SARS-CoV-2, effective disinfection of surfaces in FSEs is necessary. While disinfectants approved for use against SARS-CoV-2 are …

Development Of A Novel Fluorescent Reporter Baculovirus Vector For Testing Promoters In Lepidopterans, Daniel Howard

All Theses

Testing gene expression patterns is an important process in learning more about an organism. The standard methods of rtPCR and RNASeq provide highly detailed data on specific expression patterns, but can be resource consuming if many different samples including genes or organisms must be tested. A potential alternative for studying expression is the use of a reporter system carried by a vector system that encodes fluorescent proteins under the control of promoters of interest. Many lepidopterans (moths) are pestiferous and better understanding of gene expression levels in lepidopterans, both endogenous and exogenous including from their viruses, would be beneficial. Baculoviruses …

Cancer-Specific Perturbations To Arginine Metabolism Blunt Replication And Performance Of Oncolytic Myxoma Virus, Parker Dryja

MUSC Theses and Dissertations

Oncolytic virotherapy (OV) is a class of immunotherapy for treatment of malignancy. Using viruses that exhibit natural coincidental tropisms for cancer, or others that have been engineered to the same effect, intentional infection of lesions leads to two therapeutically beneficial effects: (1) direct destruction of the infected tumor through virally-mediated cell lysis, and (2) recruitment of an otherwise blunted or absent anti-cancer immune response to affect both local and disseminated disease. A surfeit of cancer-specific changes are accumulated during progression from first genetic insult to clinical detection, presenting a dramatically altered underlying biology of cell and tissue. The viruses employed …

Molecular Characterization Of The Antiviral Properties Of The Small Herc Family Of Proteins, Ermela Paparisto

Electronic Thesis and Dissertation Repository

Although viruses are obligate intracellular parasites, they have their own evolutionary trajectory, their genomes are in a constant battle to overcome the defenses of the host. This thesis investigates the role of the small HERC family of proteins in the battle against two deadly viruses: Human Immunodeficiency Virus -1 (HIV) and Zaire ebolavirus (EBOV). Although their discovery occurred decades ago, little knowledge is available about the small HERC family, their functions, and modes of interactions with other cellular proteins. In the first chapter, the structural evolution of the small HERC family and related functional changes that have occurred over time …

The Immune Modulation On Innate Immunity, From Pathogen Recognition To Fungal Clearance., Ko-Wei Liu

Dartmouth College Ph.D Dissertations

The human lung is not sterile but a complex environment with various microorganisms. Besides commensals in the lung, hundreds to thousands of individual microbiomes enter the lung every day but without causing the symptom. Host innate immunity plays an important role in maintaining homeostasis of the lung environment and as the first defense line against pathogens. Aspergillus fumigatus (A. fumigatus) is a saprophytic filamentous fungus that can cause human disease in immune compromised patients. However, with functional innate immunity, immune cells can quickly recognize pathogen associated molecular patterns (PAMPs) from A. fumigatus through pattern recognition receptors (PRRs). The activation of …

Characterization Of The Function And Regulation Of The Hmpv Phosphoprotein, Rachel Thompson

Theses and Dissertations--Molecular and Cellular Biochemistry

Human metapneumovirus (HMPV) is a non-segmented, negative strand RNA virus (NNSV) that frequently causes respiratory tract infections in infants, the elderly, and the immunocompromised. Despite the initial identification of HMPV in 2001, there are currently no FDA approved antivirals or vaccines available. Therefore, understanding the mechanism of HMPV replication is critical for the identification of novel therapeutic targets. A key feature in the replication cycle of HMPV and other NNSVs is the formation of membrane-less, liquid-like replication and transcription centers in the cytosol termed inclusion bodies (IBs). Recent work on NNSV IBs suggests they display characteristics of biomolecular condensates formed …

Odd Bedfellows & Marriage Of Necessity: Public Health And Politics In American Federalism, Gabriella Victoria Chianese

Honors Theses and Capstones

In the wake of the coronavirus disease 2019 (COVID-19) pandemic, while the public disagrees over mask mandates, required vaccinations, and social distancing, it seems like one common sentiment exists – a distaste for the odd bedfellows of politics and public health. There are those who cry for the compartmentalization of the science of public health and the art of politics to rectify this situation. In the wake of so much confusion and chaos, it is not unjustified to demand the depoliticization of public health; however, this response is unrealistic given the modern political climate, demonstrates a narrow understanding of the …

Dengue Virus Modulation Of Genome Instability In Vero E6 Cells, Erica Nicole Lamkin

Graduate College Dissertations and Theses

Dengue virus (DENV) is the fastest-spreading arthropod-borne virus in the world. Dengue is characterized as a major global public health challenge in tropical and subtropical nations by the World Health Organization. The number of dengue cases globally has increased 8-fold in the past two decades, with 100 to 400 million cases occurring annually. While most patients with dengue fever are asymptomatic, dengue infection carries the possibility of severe and potentially fatal febrile illness. Approximately 1 in 4 individuals infected with dengue virus develop symptomatic dengue infection, often presenting as mild to moderate, nonspecific, acute febrile illness. A smaller subset of …

Crispr Technology As An Antiviral In Dsdna And Ssrna Viruses, Cathryn Mayes

Theses & Dissertations

The COVID-19 pandemic highlights the necessity of emergency response and pandemic preparedness, especially for emerging viral threats. Currently, virus-specific vaccines and antivirals are the primary tools to combat viral diseases; however, broad-spectrum antivirals that target more than one virus species could provide additional protection from emerging and re-emerging viral diseases (Andersen et al. 2020; Zhu et al. 2015; Hickman et al. 2022).

Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated endonucleases have become recently utilized as potential antiviral strategies due to their high specificity, efficacy, and versatility (Najafi et al. 2022). While CRISPR-based antivirals have previously been used to target specific …

Biology And Ecology Of Aedes (Stegomyia) Aegypti In The Northern Chihuahuan Desert, Adam Joseph Vera

Open Access Theses & Dissertations

Aedes aegypti is a medically important mosquito species that transmits multiple arboviruses, including dengue, chikungunya, Zika, and yellow fever. This mosquito species has expanded its geographical range into expanded into the Northern Chihuahuan Desert to further increase the risk of infection by these viruses in naïve human populations. Although Ae. aegypti is abundant along the U.S.â??Mexico border, the biology and ecology of this mosquito species in this temperate/arid climate region is not understood. The objective of this study was to understand the environmental factors that influence the invasive species of Ae. aegypti abundance, breeding habitat selection, host feeding behavior, and …

Biology And Epidemiology Of Dengue Viruses In The El Paso And The Surrounding Usa And Mexico Border Communities, Pedro Miguel Palermo Infante

Open Access Theses & Dissertations

Dengue is considered one of the most important human arboviral diseases worldwide. Dengue cases have increased in the last three decades in the Americas, especially along the United States (US)- Mexico (MX) border region, where the main vector of dengue, Aedes aegypti mosquito, is widely distributed. Explosive outbreaks of dengue in northern Mexico have been associated with imported and local transmission of dengue in the US border communities, especially in the Southeast Texas area, also known as Rio Grande Valley. Due to the unknown if dengue virus (DENV) is present in other areas in the US border located west of …

Vircy-Seq : A Protocol For Characterizing Viral Activity, Tyler James Dion

Legacy Theses & Dissertations (2009 - 2024)

The main purpose of pharmaceutical production is to produce safe effective medicine for patient use. In an effort to ensure patient safety constant surveillance for viruses takes place. The detection of a viral nucleic acid in a pharmaceutical production setting results in investigations to assess its infectious potential. This is an intensive, expensive process that entails many tests such as the observation of hemadsorption, cytopathic effects (CPE), and more. These tests are typically specific and only capture certain viruses, as factors like CPE can only be observed in some viral species. A new investigational method that is effective on all …

T-Cell Antigen Receptors In Multiple Sclerosis, Lisa Lanée Keyes Jones

Biomedical Sciences Theses & Dissertations

Multiple Sclerosis (MS) is T-cell mediated autoimmune disease characterized by inflammation, demyelination, and degeneration of axons in the brain and spinal cord. A T cell-mediated immune response in MS is directed against myelin components and possibly other antigens in genetically susceptible individuals and is triggered by a viral infection. The T-cell antigen receptor (TCR) on T cells is responsible for antigen recognition and determines specificity. Our overall hypothesis is to determine whether clonally expanded T cells in patients with MS recognize viral or self-antigens and to determine whether molecular mimicry is involved in the development of the disease. To study …

Investigating The Pi3k/Akt/Atm Pathway, Telomeric Dna Damage, T Cell Death, And Crispr/Cas9-Mediated Gene Editing During Acute And Chronic Hiv Infection, Sushant Khanal

Electronic Theses and Dissertations

Human Immunodeficiency Virus (HIV) infection initiates major metabolic and cell- survival complications. Anti-retroviral therapy (ART) is the current approach to suppress active HIV replication to a level of undetected viral load, but it is not a curative approach. Newer and sophisticated gene editing technologies could indeed be a potent antiviral therapy to achieve a clinical sterilization/cure of HIV infection. Chronic HIV patients, even under a successful ART regimen, exhibit a low-grade inflammation, immune senescence, premature aging, telomeric DNA attrition, T cell apoptosis, and cellular homeostasis. In this dissertation, we investigated CD4 T cell homeostasis, degree of T cell apoptosis, an …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

Using A One Health Approach For The Assessment Of Rabies Control In Rural Victoria Falls, Zimbabwe, Ryan Lapenna

Electronic Thesis and Dissertation Repository

Rabies, a viral zoonotic disease, is widespread in Zimbabwe, with human fatalities reported annually in the country. To supplement the Government’s effort on rabies control, the Victoria Falls Wildlife Trust and Veterinarians for Animal Welfare Zimbabwe have joined forces to carry out dog rabies vaccinations in rural communities adjacent to the major tourist attraction of The Victoria Falls. A One Health approach was used to 1) determine the level of protective rabies antibodies among a sample of rural dogs and 2) collect information and describe the knowledge, attitudes, and practices related to rabies among dog owners. In 2020, blood was …