The current Coronavirus disease 2019 (COVID-19) outbreak, caused by a virus called severe acute respiratory syndrome 2 (SARS-CoV-2), has become a global health emergency. Recent findings in case studies assert that the transmigration of SARS-CoV-2 to the nervous system implicates severe neurotropic pathologies, including the onset of the rare autoimmune disease called Guillain-Barré syndrome (GBS). GBS is recognized as several disorders characterized by immune-mediated polyradiculoneuropathy, which is typically preceded by an infection or other immune stimulation. The symptoms of GBS initially present as acute symmetrical ascending paresthesia, weakness, and paralysis. This meta-analysis serves to help understand the predisposing factors (such as gender, age, comorbidities) and the clinical features of COVID-19- induced GBS. Most patients affected were 40 years or older and comprised 78.2% of all the cases. Males comprised most of the cases (62.8%; n=76). The patient mortality was 9.1%, intensive care unit (ICU) admission was 46.6%, and the need for mechanical ventilation was 35.8%. It was found that concomitant GBS and COVID-19 patients most often presented with increased cerebral spinal fluid (CSF) protein levels (88%; n=106), hyporeflexia or areflexia (87.6%) (n=106), lower limb strength and sensation impairment (91.7%; n=111), upper limb strength and sensation impairment (83.5; n=101), and somatic sensation impairment (73.6%; n=89). It is postulated that COVID-19 triggers the onset of GBS through a “cytokine release storm” (CRS) that occurs in the early stages of the disease. The same cytokines and chemokines involved in this CRS caused by COVID-19 contribute to the onset of GBS. Predisposing factors which influence this concomitance include male gender and older age. Most of the reported symptoms included abnormal limb functions (including paresthesia, weakness, and paralysis) and absent or weak deep tendon reflexes. The most common variant of GBS observed was AIDP, and the most significant laboratory finding among patients was high CSF protein levels.

The COVID-19 pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2, or SARS-CoV-2, has been ongoing for over two years. The virus spreads easily and is more unpredictable than well-known viruses like the flu, making it important to have reliable combative measures before we fully drop non-vaccine preventive actions, like mask-wearing.Therefore, we used computational protein modeling to investigate the interactions of three nonstructural proteins (abbreviated Nsp) encoded in the viral RNA genome– Nsp3, Nsp5, and Nsp6 – which are involved in the viral life cycle, with human P-type polyamine transporting ATPases ATP13A2 and ATP13A3, whose disease symptoms when mutated mimic certain COVID-19 complications. Understanding these interactions can help shed light on the mechanism of unexpected symptoms seen in COVID-19 and provide an avenue through which to treat infections. Additionally, papain-like protease (PLpro) and 3-chymotrypsin-like protease (3CLpro), which correspond to Nsp3 and Nsp5, respectively, are highly conserved between SARS-CoV and SARS-CoV-2 and thus make good potential drug targets due to their active sites and presumable lower ability to tolerate mutations (reducing the likelihood of treatments becoming ineffective), although the potential effects on the human proteasome would need to be further investigated. In addition, Nsp6 may help the virus evade host defenses by limiting the ability of autophagosomes to deliver viral particles to lysosomes, so limiting its interactions may increase the ability of the host cell to target its viral invader. One compound in particular, Haloperidol, showed promising results; predicted docking (via computational molecular docking software) to Nsp6 alone, as well as to Nsp6-heteroprotein complexes suggested strong binding, indicating a potential strong interaction that could impact the viral protein function and thus the viral life cycle.

The purpose of this study was to focus on whether solely obesity (measured by BMI) leads to an increased risk of COVID-19 mortality in terms of excess in-hospital deaths. As the grim milestone of one million deaths in the United States from COVID-19 was reached, one could assume the disease would continue to coexist with humanity in the long term. While vaccination continued to limit the spread of COVID-19, it was essential to investigate risk factors that may exacerbate the severity of the illness in humans. Obesity is already a global pandemic affecting 40% of Americans and over 650 million people worldwide. Obesity is connected to an entire range of clinical conditions including some of the leading causes of death worldwide making it a more generalizable statistic. Furthermore, the purpose of this study was to conduct a systemic review of major risk factors between obesity and COVID-19, and this analysis shall ascertain which factors have the most predictive value in determining mortality and severity of the condition. Ten research studies of 3,780,926 COVID-19 patient cases were included. Meta-analysis results indicate a pooled OR of 0.93 (0.71-1.23, p = 0.627) for in-hospital mortality of obese patients relative to non-obese patients when adjusted for confounders. All comorbidities associated with the development of severe disease were found to have an equal chance of leading to mortality. In other words, obesity did not lead to a statistically significant risk of dying from COVID-19.

I december 2019 i Wuhan, Kina, blev en grupp personer infekterade av det nya viruset SARS-CoV-2 som inducerade sjukdomen COVID-19. Sjukdomen påverkar lungfunktionen och studier har visat att långvarig påverkan på lungfunktionen kan förekomma. Syftet med den aktuella studien var att undersöka långvariga effekter av COVID-19 på diffusionskapaciteten i lungorna. Studier som undersökte diffusionskapaciteten, mätt med kolmonoxid (DLCO), hos patienter minst 30 dagar efter insjuknande i COVID-19 samlades in och analyserades. Resultatet visade att en stor del av deltagarna hade DLCO <80% av det förväntade värdet. Det visade även att diffusionskapaciteten kan vara nedsatt upp till sex månader efter utskrivning från sjukhus. Då COVID-19 är en ny sjukdom var den aktuella studien begränsad av antalet studier inom området. Framtida studier bör undersöka effekterna av COVID-19 på lungfunktionen under ett längre tidsspann. Slutsatsen i den här litteraturstudien var att COVID-19 påverkar diffusionskapaciteten i lungorna. Långvariga nedsättningar i diffusionskapaciteten har, än så länge, kunnat påvisas upp till sex månader efter sjukdom. Allvarligt insjuknande i COVID-19 ökar risken för långvariga DLCO -nedsättningar.

As obligatory intracellular parasites, viruses are in a constant battle with their host to establish infection. They can facilitate their propagation by modulating host immune or metabolic pathways. This modulation involves targeting various molecular factors such as microRNAs (miRNA), enzymes, or small molecules. Understanding how viruses alter the chemical makeup of a cell is crucial to identifying what pathways are being targeted, furthering our understanding of the virus life cycle, and may aid in identifying biomarkers of disease. Here, we examine host-virus interactions in the context of two viruses, hepatitis c virus (HCV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). First, the modulation of serine hydrolases by a pro-viral microRNA, miRNA-122, is investigated using activity-based protein profiling (ABPP). This study identifies a downstream target of miRNA-122 that is differentially activated during HCV infection which can be targeted pharmacologically to reduce HCV infectivity. Second, we apply similar techniques to identify serine hydrolase changes associated with SARS-CoV-2 infection. Results point towards enrichment of endocannabinoid metabolism which may offer an alternative therapeutic avenue for combating SARS-CoV-2 infection. Together, the work presented in this thesis provides avenues for further investigation into miRNA-122 interactions during HCV infection and endocannabinoid metabolism in SARS-CoV-2 infection.

Unexpected high mutations detected in new emerging variants of concern (VOCs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially in the case of omicron, raises concerns and efforts to understand their evolutionary trajectory. Several hypotheses have been discussed in literature to conceptualize the source of their emergence, including intra-host viral evolution in immunocompromised patients. These patients grant opportunities for the emergence of new variants through a persisting virus winning against host immunity, and selection for viral mutations driven by treatment interventions. VOCs have in common high mutation rate exceeding the average rate of 1-2 mutations per month. Not many studies have investigated the evolutionary rate of SARS-CoV-2 in immunocompromised candidates. Therefore, the purpose of this study is to reveal potential mechanisms underlying the emergence of VOCs by exploring substitution rate of SARS-CoV-2 genomes from surveyed COVID-19 immunocompromised patient’s studies. First, SARS-CoV-2 genome sequences were collected at sequential time series throughout host infection, which were reported in the previous studies. Filtration criteria was applied to reanalyze patients with prolonged infection documented for ≥ 2 months, and comprehensive sequenced samples for ≥ 6 time points. Then, phylogenetic analysis was conducted using Nextclade (https://clades.nextstrain.org/), followed by mutation rate analysis using two substantial similar approaches to calculate the rate in i) substitutions per month and ii) substitutions per site (per year). The mutation tendency of SARS-CoV-2 in immunocompromised hosts was compared to reported VOCs, particularly to omicron. The highest observed mutation rate accounted for approximately 2.2 mutations per month, which is higher than the average rate. High mutation rate was due to prolonged infection and selection pressure by treatment interventions (i.e., convalescent plasma and antibodies). Here, higher rate of intra-host viral evolution in immunocompromised patients is detected, potentially leading to the emergence of VOC. Hence, this research highlights the need for sequencing efforts in high-risk individuals, updating treatment strategies along with further analysis on adaptive mutants pronounced due to intra-host evolution. Together, such findings provide an ultimate synergy for future public health guidelines and infection control measures.

<p>  </p> <p>Seven-membered ring structures are one of the most important structural motifs found widely in natural products and bioactive molecules. Although several [5+2]-cycloaddition reactions have been developed to construct these seven membered cores, asymmetric cycloaddition reactions are less explored. Described in Chapter-1 is a base mediated intramolecular diastereoselective [5+2]-cycloaddition reaction that afforded highly functionalized seven membered rings in good yields and excellent diastereoselectivities. The high diastereoselectivity is controlled by the alkyl stereocenter and the chain length of the alkene tether. The existing chirality of the substrate can direct the stereochemical outcome of the [5+2]-cycloaddition reaction. Furthermore, this methodology has been applied to synthesize various potent HIV-1 protease inhibitors. </p> <p>COVID-19 pandemic has profoundly affected life around the globe and costed us 6 million lives. Therefore, there is an urgent need for rational design of new drug candidates to specifically target different SARS-CoV-2 proteins. Recently, Pfizer developed an FDA-approved antiviral therapeutic agent, Paxlovid, targeting SARS-CoV-2 3CLpro. Chapter-2 discusses a concise synthetic route to synthesize active component of Paxlovid, Nirmatrelvir, in 6-steps without any epimerization. We have also developed a series of potent covalent inhibitors targeting SARS-CoV-2 3CLprotease and compared the antiviral activities of these inhibitors with that of Nirmatrelvir. </p> <p>In the final chapter, a concise partial synthesis of the segment A of (-)-Rafonin is discussed. (-)-Rasfonin is an antitumor agent that induces apoptosis in <em>ras</em>-dependent cells. We have proposed an asymmetric chiron approach to install the α-pyranone ring of rasfonin. Our goal is to perform SAR studies on this natural product by designing various analogues. </p>

All cells depend on properly folded proteins for survival and function. Misfolding of proteins results in loss of critical functions and may trigger the misfolding of other nearby proteins leading to toxic aggregation. While many proteins can fold on their own, others with complicated domain structures require assistance from protein folding machines called chaperones. The most complex and highly specialized of all chaperones is the eukaryotic chaperonin complex CCT which is necessary for the folding of a wide variety of essential proteins. These include the cytoskeletal proteins actin and tubulin as well as the Gβ subunit of the G protein heterotrimer. However, CCT activity can also drive diseases such as cancer and viral infections and could represent a high value therapeutic target if the mechanisms by which it folds its different client proteins were better understood. To this end, we identified and characterized an interaction between CCT and the RNA-dependent RNA polymerase of SARS-CoV-2, the virus responsible for the deadly global pandemic that began in 2019. We showed that SARS-CoV-2 replication is impaired by loss of CCT and that the polymerase, designated Nsp12, interacts with CCT upon synthesis and quickly releases - the hallmark pattern of a CCT substrate. Furthermore, we solved a 3.3 Å cryo-EM structure of Nsp12 bound to open CCT showing Nsp12 binding between the two rings of CCT and extending up through of the folding chambers and out of CCT. At 107 kD, Nsp12 is the largest substrate ever visualized inside of CCT and answers a long-standing question in the field of how CCT could accommodate substrates larger than its 70 kD folding chamber. Given that CCT is known to fold proteins with WD40-repeat domains, we also investigated a potential relationship between CCT and RPE65. RPE65, which contains a WD40 domain, is the retinyl ester isomerase that converts all-trans retinyl esters into 11-cis retinol, a key step in the visual cycle, and its mutation is a common cause of hereditary retinal dystrophies. We showed that CCT interacts with RPE65 and that nascent RPE65 binds and releases from CCT albeit with relatively slow kinetics. However, RPE65 is not dependent on CCT for expression or activity. This suggests that the relationship between RPE65 and CCT may represent a novel CCT function distinct from the canonical obligate substrate dynamic.

Antimicrobial resistance (AMR) threatens our modern standard of living with the potential return to a pre-antibiotic condition where deadly infections are no longer treatable. Wastewater treatment plants (WWTPs) are vital components in water sanitation infrastructure and are now also being recognized as valuable monitoring points for antibiotics, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) disposed of or excreted by human populations. Hospital waste water is of special interest as a potential focused monitoring point and in general research is needed to establish the benefits of both on-site and community-scale wastewater treatment as important barriers to the disseminators of ARGs into the environment. The research aims described herein examine these components of wastewater treatment and how they relate to AMR indicators identified through metagenomic sequencing. Through monitoring of local WWTPs, it was found that AMR indicators shifted over time and in relation to human behavior that changed due to the COVID-19 pandemic. Hospital wastewater did not measurably impact the microbiome during simulated activated sludge wastewater treatment according to broad-scale metagenomic ARG profiling; however, some clinically-relevant ARGs escaped treatment. Lastly, a study of a transect of WWTPs indicated impacts on the abundance of certain ARGs in downstream riverine receiving environments. Nonetheless, there appeared to be a number of other factors at play, and upstream and downstream resistomes tended to remain similar, calling for further research to delineate impacts of various wastewaters and treatments on ARGs in affected aquatic environments. / Doctor of Philosophy / Antimicrobial resistance (AMR) occurs when bacteria, viruses, and fungi are able to survive in the presence of antibiotics because they carry antibiotic resistance genes (ARGs) encoded in their DNA. AMR is a major public health concern as it makes it so that antibiotics are no longer effective against potentially deadly infections. Wastewater treatment plants (WWTPs) are being discovered as a hub of opportunity for monitoring potential AMR problems in a community. WWTPs receive sewage from homes and various industries. This sewage contains rich information for researchers to examine in terms of which antibiotics, bacteria, and ARGs are circulating in the community. This makes it possible to find out which antibiotics are being consumed in the community and which ARGs might be prevalent. The purpose of this research was to better understand both how WWTPs can be used as monitoring points for AMR and how they can be improved to help reduce ARGs emitted to rivers and streams where treated water is discharged. It was found that the types of ARGs prevalent in wastewater changed over time, especially during the COVID-19 pandemic as people worked from home and changed habits regarding doctors' visits, which impacted antibiotic use. Hospital sewage was studied as a useful indicator of pathogens and ARGs that are challenging a community and also the antibiotics being used. This research explored what happened to ARGs during the treatment of domestic (i.e., from people's homes) wastewater along with hospital wastewater and found that hospital wastewater introduced some ARGs that are typically found in clinical settings, but did not negatively impact the overall wastewater treatment process. Finally, the impact that WWTPs have on rivers to which treated water is discharged was explored. The results indicated that certain ARGs were elevated downstream of the WWTPs. However, when examining all ARGs together, no major shifts due to the treated wastewater were apparent.

La pandémie de la COVID-19 a été causée par le virus SARS-CoV-2. Il est maintenant compris que ce virus peut être transmis par des aérosols émis par une personne infectée vers une personne saine. En raison de ce type de transmission, les environnements de soins de santé tels que les hôpitaux et les centres de soins de longue durée doivent protéger leurs patients, mais aussi leurs travailleurs. Pour ce faire, les patients sont hébergés dans des chambres à pression négative qui empêchent l'air contaminé de sortir de la pièce sans être filtré. L'objectif de cette étude est d'identifier l'exposition des travailleurs au virus SARS-CoV-2 à l'intérieur et à l'extérieur de la chambre du patient. Le premier objectif de cette étude était de caractériser l'émission virale des patients positifs à la COVID-19. Des échantillons d'air ont été collectés sur une période de 24 heures à l'intérieur des chambres des patients positifs. Les données cliniques des patients échantillonnés ont été recueillies par le personnel de santé pour tenter de prédire les variations des taux d'émission des patients. Le deuxième objectif de l'étude était d'évaluer la contamination de l'air à l'extérieur des chambres des patients. Des surfaces ont été utilisées comme indicateur indirect de la contamination de l'air. Ces surfaces ont été échantillonnées avant et pendant 6 semaines consécutives après le nettoyage pour analyser l'évolution de la contamination virale dans le temps. L'ARN de SARS-CoV-2 était présent dans 63,7 % des échantillons d'air collectés, et le taux moyen d'émission était mesuré à 1,11E+06 génomes/personne/heure. Aucune donnée clinique collectée n'avait de relation significative avec le taux d'émission des patients. L'échantillonnage de surface montre une quantité détectable d'ARN viral sur 4 des 15 surfaces, et aucune contamination jusqu'à 6 semaines après le nettoyage. La détection de l'ARN viral dans l'air des chambres des patients, mais l'absence de facteurs expliquant les variations des taux d'émission observés, confirme la nécessité de comprendre l'émission du virus par les patients pour mieux protéger les travailleurs de la santé. L'échantillonnage de surface effectué à l'extérieur des chambres indique que l'isolement des patients positifs au virus de la COVID-19 dans des chambres à pression négative a empêché l'air contaminé de quitter la pièce, protégeant ainsi les travailleurs à proximité. / The COVID-19 pandemic is a global health crisis caused by the SARS-CoV-2 virus. It is now understood that the virus can be transmitted by aerosols emitted from an infected person to a healthy one. Because of this type of transmission, healthcare environments like hospitals and long-term care centers need to protect their patients but also their workers. To do this, patients are housed in negative pressure rooms that prevent contaminated air from exiting the room without being filtered. The goal of this study was to characterize the SARS-CoV-2 virus exposure to workers inside and outside the patient's room. The first objective of this study was to characterize viral emission from COVID-19 positive patients. Air samples were collected for a period of 24 hours inside positive patient's rooms. Clinical data of patients in the sampled rooms were collected by healthcare staff to try to predict variations in patient's emission rates. The second objective of the study was to evaluate the air contamination in zones outside of patient's rooms. Surfaces were used as an indirect air contamination indicator. These surfaces were swabbed before and for 6 consecutive weeks after cleaning to analyze the evolution of the contamination through time. SARS-CoV-2 RNA was present in 63.7% of the air samples collected and the mean emission rate was measured at 1.11E+06 genomes/person/hour. No collected clinical data collected was associated to patient emission rate. Surface swabbing showed detectable quantity of viral RNA on 4 of the 15 surfaces and no contamination up to 6 weeks after cleaning. The detection of viral RNA in the air of patients' rooms but the lack of factors explaining the variations in emission rates observed confirms the need to better understand virus emission by patients to better protect healthcare workers. Surface sampling outside the rooms indicated that the isolation of patients positive for SARS-CoV-2 in negative pressure rooms prevented contaminated air from leaving the room, thereby protecting healthcare workers.