Medicine and Health Sciences Commons^™

Mining Sars-Cov-2 Phylogenetic Trees To Estimate Circulating Infections And Patterns Of Migration, Erin V. Brintnell

Electronic Thesis and Dissertation Repository

The SARS-CoV-2 pandemic led to the formation of very large databases of genomic viral data. These databases contain information on transmission dynamics, emergence and evolution of SARS-CoV-2. However, extracting this information from sequences is difficult, as most methods of analyzing viral genomes were developed for smaller data sets. Therefore, my objective was to develop new fast estimators of the number of infections (I) and the rate of migration based on simple features of SARS-CoV-2 phylogenies.

I simulated pathogen evolution using a susceptible-exposed-infectious-recovered (SEIR) model of pathogen spread, reconstructing evolution using CoVizu. For simulations of I, I varied the total number …

The Effect Of Oral And Topical Antibiotics On Foreskin Inflammation And Hiv Target Cells In Ugandan Men., Zhongtian (Eric) Shao

Electronic Thesis and Dissertation Repository

Penile circumcision reduces HIV susceptibility by up to 60% in men; however, many men prefer to remain uncircumcised for personal or cultural reasons. Penile circumcision protects against HIV by reducing anaerobic bacteria on the penis. Penile anaerobes cause local inflammation and the recruitment of HIV-susceptible CD4+CCR5+ cells, increasing the likelihood that exposure to HIV during intercourse results in infection. To determine if a non-surgical intervention can reduce penile anaerobes and HIV target cells, we randomized men to antimicrobial treatment prior to circumcision. To be able to quantify the effect of antimicrobials, we developed a novel deep-learning algorithm to quantify HIV …

A Theoretical Perspective On Parasite-Host Coevolution With Alternative Modes Of Infection, George N. Shillcock

Electronic Thesis and Dissertation Repository

We investigate how natural selection shapes the coevolution of parasitism. We discuss the antagonism fuelled by parasites’ necessity to transmit to novel hosts, and host’s desire to minimise virulence. In support, we build a mathematical model which considers the epidemiology and life-history trade-offs faced by an obligate microparasite and its host. Our model allows parasites to be transmitted to new hosts via direct contact (horizontally) or from parent to offspring during birth (vertically). We test the hypothesis that vertical transmission causes virulence to diminish in the long run, and contrary to widely accepted views, find that vertical transmission need not …

Hiv-1 Drug Resistance To Integrase Strand Transfer Inhibitors In Hiv-1 Non-B Subtypes, Emmanuel Ndashimye

Electronic Thesis and Dissertation Repository

Human immunodeficiency syndrome (HIV-1) has infected over 75 million people and over 35 million have succumbed to virus related illnesses. Despite access to a variety of antiretroviral therapy (ART) options, ART programs have been disproportionally spread in the world with low-and middle-income countries (LMICs) facing challenges to access the most potent ART options. With less potent ART remaining in use in LMICs, HIV-1 drug resistance (HIVDR) presents a growing challenge in LMICs. Since approval of the first-generation integrase strand transfer inhibitor (INSTIs), Raltegravir (RAL) in 2007, INSTIs remain the best choice as a backbone of ART. Access to second generation …

Development And Evaluation Of A Heterogenous Virus-Like Particle (Vlp) Formulation To Achieve Hiv-1 Latency Reversal And Cure., Joshua P. Pankrac

Electronic Thesis and Dissertation Repository

HIV-1 is the etiological agent behind acquired immune deficiency syndrome (AIDS) – a chronic, life-threatening condition that compromises host immune function. After nearly four decades and despite ongoing global efforts, HIV-1 persists in nearly 38 million individuals worldwide. Of this population, only 60% have access to life-saving combination antiretroviral therapy (cART), clearly emphasizing the need to realize a cure. Unfortunately, the establishment of replication-competent provirus in resting CD4+ T lymphocytes represents a significant barrier to HIV-1 curative research. The viral reservoir is highly stable and has a half-life of ~44 months. Therefore, it is unlikely that infection will naturally exhaust …

Utilizing Fiv (Feline Immunodeficiency Virus) To Develop A Novel Animal Model To Study Hiv (Human Immunodeficiency Virus), Ankita Suryakant Kambli

Electronic Thesis and Dissertation Repository

This project sought to perform the in vitro work needed to accomplish the long-term vision of harnessing the similarities between HIV (Human Immunodeficiency Virus) and FIV (Feline Immunodeficiency Virus) to develop an animal model whereby cats can be used to study HIV pathogenesis and therapeutics. We transfected CRFK (Crandell Rees Feline Kidney) fibroblasts with plasmids that could express human or feline CD4, CCR5, or both, and determined receptor surface expression through flow cytometry. We discovered that HIV envelope expressed on 293T can fuse with huCD4/huCCR5 on CRFK. These cat cell lines were also capable of supporting HIV infection. Additionally, we …

Virally Packaged Rna In Virus-Like Particle Vaccines Enhances Antigenicity And Augments Latency Reversal Of Hiv-1, Chanuka Wijewardhana

Electronic Thesis and Dissertation Repository

Introduction:

Since Human Immunodeficiency Virus (HIV)-1 was determined to be the etiological agent behind acquired immunodeficiency syndrome (AIDS) in 1983, numerous attempts at a cure have been made; however, none have been effective. One of the primary roadblocks in achieving a cure is a transcriptionally-silent latent reservoir of memory CD4+ T cells harboring HIV provirus. Combined antiretroviral therapy (cART) inhibits actively replicating virus by interfering with various stages of the replication cycle. Therefore, non-replicative viruses–like the proviruses found in latently infected cells–are hidden from the actions of continued antiretroviral therapy. As a result, cART discontinuation or treatment holidays can result …

Determining The Relative Transmission Fitness Of Hiv-1 Subtypes A, B, C, And D, Spencer Yeung

Electronic Thesis and Dissertation Repository

There is in vivo evidence that suggests the genetic diversity of HIV-1 subtypes influence heterosexual transmission efficiency. To recapitulate sexual transmission in vitro, blocks of genital tissue were exposed to mixtures of genetically different subtype viruses. Migrating immune cells were collected and co-cultured with a CD4+ T-cell line permissive to HIV infection (PM1) to measure dendritic cell virus transfer; HIV-exposed tissues were cultured separately. Next generation sequencing (NGS) of HIV-1 DNA was used to quantify relative infection rates of the various challenge viruses, and to assess fitness differences in infection of the tissue vs. migratory/T cell co-cultures. Our results …

Designing An Optimal Hiv-1 Env Immunogen For The Vesicular Stomatitis Virus Vaccine Platform And Elucidating The Role Of Hiv-1 Nef In Env Trafficking, Jason Knapp

Electronic Thesis and Dissertation Repository

Current vesicular stomatitis virus (VSV)-based HIV vaccines require an optimal HIV envelope immunogen to improve protection in vivo. Furthermore, the involvement of viral proteins, such as HIV Nef, in the trafficking of HIV Env to sites of viral assembly remains poorly understood and may provide additional insights for the design of a VSV-based HIV vaccine. We constructed new codon-optimized chimeric Env immunogens containing the signal sequence of honeybee melittin and the transmembrane and cytoplasmic tail domains of SIV, Zaire Ebola, or VSV glycoproteins. We showed that all chimeric Env immunogens had enhanced expression levels within producer cells. Utilizing bimolecular …

Hiv-1 Group M Subtype Fitness, Disease Progression, And Entry Efficiency, Colin M. Venner

Electronic Thesis and Dissertation Repository

Human immunodeficiency virus type 1 (HIV-1) emerged in the human population shortly after the turn of the 19th century. Distribution of HIV-1 across the globe over the past 30–35 years can be traced to founder events with primordial HIV strains from sub-Saharan Africa. Even considering the burden of HIV in Africa, our knowledge of HIV-1 disease is still largely limited to subtype B HIV-1, a strain responsible for 3 million infections in North America and Europe as compared to the 33 million that are infected with HIV-1 subtypes A, C, D, and circulating and unique recombinant forms.

This dissertation analyzes …

Effect Of Bacterial Superantigens On The Magnitude And Breadth Of Influenza-Specific Cd8+ T Cell Responses, Courtney Meilleur

Electronic Thesis and Dissertation Repository

Severe cases of influenza A virus (IAV) infection are often complicated by concomitant bacterial pneumonia or sepsis. Many bacterial species are capable of producing potent immunomodulators called superantigens (SAgs), which have the potential to interfere with cell-based antiviral immune mechanisms. I asked what effects bacterial SAgs have on both the magnitude and the breadth of antiviral CD8⁺ T cell (TCD8⁺) responses. Surprisingly, administration of SAgs to mice shortly before or after vaccination with IAV increased the number of primary TCD8⁺ responding to select IAV-derived epitopes. T cell receptor staining of these SAg-augmented populations revealed expression of …

Evaluating The Conservation Of Rna Packaging Enhancer Elements Across Lentiviruses, Seyed Arad Moghadasi

Electronic Thesis and Dissertation Repository

It was previously thought that the RNA structural elements within the 5’UTR were the sole determinants of RNA packaging in HIV-1. However, in 2013 Chamanian et al. discovered that the region overlapping the Ribosomal Frameshift Signal (RFS) acted to enhance RNA packaging 50 fold and was thus named the genomic RNA packaging enhancer element (GRPE). To determine if the GRPE was conserved across lentiviruses, using the same approach as Chamanian et al., deletions in similar regions of the SIVmac239 and FIV 34TF10 genomes were done to measure their impact on RNA packaging. No region across the gag-pol ORF of SIVmac239 …

Understanding The Impact Of Hiv-1 Genetic Diversity On The Function Of Nef And Its Role In Serinc5 Antagonism, Aaron Leslie Johnson

Electronic Thesis and Dissertation Repository

HIV-1 Nef is a key pathogenic protein, allowing HIV-1 to evade the host immune system by downregulating MHC-I and CD4. Furthermore, it was recently discovered that Nef counteracts the host factor SERINC5 to increase HIV-1 infectivity, but the mechanistic details of the Nef:SERINC5 interaction still need to be explored. Throughout this dissertation, I will explore the hypothesis that the genetic diversity that defines HIV-1 has a pronounced effect on the HIV-1 protein Nef, altering its function between and within group M subtypes. To address this hypothesis I investigated how MHC-I and CD4 downregulation differ among all non-recombinant group M subtypes. …

The Epidemiology Of Infective Endocarditis Among People Who Inject Drugs In London, Ontario., Brian Hallam

Electronic Thesis and Dissertation Repository

Infective endocarditis is an infectious disease that affects the valves of the heart. Injection drug use is currently a leading risk factor among patients with endocarditis. We conducted a prospective study using data from hospital chart records among patients with endocarditis in London, Ontario, which has a relatively high prevalence of people who inject drugs to assess the severity of the issue and the major risk factors of mortality pertaining to this population. This study had a sample size of 353 and included a review of the incidence of admissions of endocarditis, as well as a survival analysis, using both …

Risk Factors For Bk Virus Infection After Kidney Transplantation, London, Ontario 2016, Seyed M Hosseini-Moghaddam

Electronic Thesis and Dissertation Repository

Our objective was to determine the risk factors for BK virus infection in renal allograft recipients in the first year after transplantation. In this cohort, we included all patients who received renal allograft at London Health Sciences Centre (LHSC) between 2012 and 2014. We continued post-transplantation follow-up for one year. Of 175 patients (37% female) with median age (range) of 53 (14-82) years, 40 (22.9%) developed BK viremia (median interval:100 days, range: 35-264). Recipient age, recipient gender, hemodialysis (HD) vs peritoneal dialysis (PD), Human Leukocyte Antigens A1, B35 and Cw4 increased the risk of post-transplant BKV infection. However, donor gender, …

Genomic Predictors Of Drug Response To The Alpha-Specific Phosphoinositol 3-Kinase (Pi3ka-Alpha) Inhibitor Byl719 In Head And Neck Cancers, Giananthony T. Rizzo

Electronic Thesis and Dissertation Repository

PIK3CA is the only frequently mutated, druggable oncogene in head and neck squamous cell cancer (HNSCC), with PIK3CA point mutations and gene amplification rates of 17.5% and 40% respectively, with higher rates in HPV-positive disease. The objective of this research was to determine the effects of BYL719, an α-specific PI3K inhibitor in HNSCC cell lines.

All cell lines with PIK3CA hotspot point mutations or gene amplifications will be sensitive to BYL719.

Twenty-eight HNSCC cell lines were subjected to increasing concentrations of BYL719 and cell viability was measured over time. Cell lines were screened for activating PIK3CA hotspot mutations and amplifications …

Human Adenovirus E1a Binds And Retasks Cellular Hbre1, Blocking Interferon Signalling And Activating Virus Early Gene Transcription, Gregory J. Fonseca

Electronic Thesis and Dissertation Repository

Upon infection, human adenovirus (HAdV) must block interferon signaling and activate the expression of its early genes to reprogram the cellular environment to support virus replication. During the initial phase of infection, these processes are orchestrated by the first HAdV gene expressed during infection, early region 1A (E1A). E1A binds and appropriates components of the cellular transcriptional machinery to modulate cellular gene transcription and activate viral early genes transcription. We have identified hBre1/RNF20 as a novel target of E1A. hBre1 is an E3 ubiquitin ligase which acts with the Ube2b E2 conjugase and accessory factors RNF40 and WAC1 to monoubiquitinate …

Restriction Of Hiv-1 Replication By Unique Trim22 Isoforms., Clayton Hattlmann

Electronic Thesis and Dissertation Repository

Understanding how the immune system reacts to HIV infection and why normal antiviral defenses are insufficient to fight infection is a key step towards creating better therapies. Several interferon-induced proteins, such as the tripartite motif protein TRIM22, are capable of restricting HIV-1 replication; however single nucleotide polymorphisms (SNPs) can dramatically impact the actions of these proteins. While the trim22 gene contains numerous SNPs, no study has addressed how these may affect TRIM22 functions. Here we provide the first direct comparison of two TRIM22 unique isoforms. Through confocal microscopy we observed these isoforms exhibit different patterns of localization. In vitro studies …