Saudi Cultural Missions Theses & Dissertations
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Item Restricted Investigating the impact of coronavirus infections on the host respiratory microbiome(University of Liverpool, 2024-05) Alrezaihi, Abdulrahman; Hiscox, JulianCoronaviruses, including the recent SARS-CoV-2, present a complex challenge for public health due to their ability to cause illnesses ranging from asymptomatic infection to patients suffering severe symptoms and death. This thesis employed advanced sequencing methods to identify and study different coronaviruses, from seasonal varieties to MERS-CoV and SARS- CoV-2, and their interactions with the host microbiome in both human clinical samples and animal models. This was underpinned by Oxford Nanopore long-read sequencing combined with modifications of sequence-independent single primer amplification (SISPA). This research aims were to improve the ability to detect coronaviruses, particularly in samples with low viral loads, by modifying different enrichment methods that were designed to detect SARS-CoV-2, identify lineages, and simultaneously define the nasal microbiome. The study revealed changes in the microbiome of patients with coronavirus infections, showing how the virus and the nasal microbiome interact. The data indicated that certain bacterial populations were more predominant in specific groups of patients with COVID-19 or MERS, potentially affecting the course of their illness. The investigation showed that dysbiosis, or microbial imbalance, was significant within coronavirus infections and occurred irrespective of the virus type (MERS-CoV or SARS-CoV-2) and mortality outcome. The investigation compared these patterns in human patients with those observed in a mouse model of SARS-CoV-2 that recapitulated severe disease. This study specifically identified differences in the microbiome between the upper and lower respiratory tracts. Examining the lower respiratory tract in humans is not common as this involves invasive sampling, and use of samples from intensive care patients facilitated this research. This comparison clarified how SARS- CoV-2 affected various parts of the respiratory system and showed that changes in viral load affected the microbiome composition within these distinct areas. Furthermore, the study defined how the microbiome changed throughout the infection, particularly in patients with severe illness who required intensive care.38 0Item Restricted Investigation of the roles of MERS-CoV accessory proteins: ORF4a and ORF4b with the host(University of Liverpool, 2024-03-05) Almsaud, Mai; Hiscox, JulianCoronaviruses account for a high burden of respiratory disease in humans, ranging from common colds to severe acute respiratory syndrome. The emergence of severe acute respiratory syndrome (SARS) in 2002, Middle East respiratory syndrome (MERS-CoV) since 2012 and, more recently, SARS-CoV-2 have attracted considerable attention worldwide. The persistence of sporadic MERS-CoV cases, along with the absence of vaccines and antivirals, and the strikingly high morbidity and mortality rate of 36%, underscore the ongoing risk posed by MERS-CoV to global health security. Nevertheless, gaining a comprehensive understanding of the pathogenic significance of MERS-CoV requires further research. As viral replication and infection rely on the host cell machinery for the viral life cycle, studying how cells respond to infection allows us to understand the mechanisms involved in either limiting virus infection or, when control fails, in pathogenesis. In contrast, viruses can encode specific proteins to counteract these host responses. MERS-CoV ORF4a and ORF4b are two such proteins and recognised for their roles in modulating the host immune system, thereby influencing viral pathogenicity. This study investigated the significant roles of MERS-CoV accessory proteins, ORF4a and ORF4b, using two distinct high-throughput methods: a label-free mass spectrometry proteomics approach and a transcriptomic approach based on long-read cDNA-PCR sequencing. The proteomic approach unveiled novel interactions between MERS-CoV ORF4a, ORF4b, and host factors. Complementing the LC-MS/MS analysis, long-read length Nanopore sequencing was employed to explore the transcriptomic landscape influenced by MERS-CoV ORF4b expression. This technique allowed for a comprehensive assessment of isoform usage and mRNA regulation, providing novel insights into the virus hijacking splicing machinery by ORF4b. The investigation of both viral proteins, ORF4a and ORF4b, was extended by comparing their relative strengths in subverting the innate IFN-β response with those of similar proteins encoded by other coronaviruses. This demonstrated the distinct potency of MERS-CoV ORF4a and ORF4b proteins in relation to the severity of MERS disease when compared to other coronaviruses. Collectively, this thesis contributes to the understanding of the interactions that MERS-CoV establishes with its host, highlighting the significance of accessory ORFs in pathogenesis, and emphasising their potential as subjects for ongoing monitoring.39 0