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.

<p dir="ltr">The emergence of infectious diseases like HIV, influenza, and COVID-19 highlights the urgent need for highly scalable testing methods that can be deployed outside traditional laboratory settings. Despite decades of research in point-of-care (POC) diagnostics, the main challenge remains the limited performance of assays, especially in terms of sensitivity. Furthermore, most POC assays originating from academic research struggle to transition beyond the laboratory due to manufacturability issues. This dissertation aims to enhance the effectiveness of viral molecular detection platforms for POC diagnostics by improving analytical and clinical sensitivity and facilitating the practical adaptation of academic-developed POC devices for use outside laboratory settings.</p><p dir="ltr">Each aim addresses a separate aspect of device development. The first aim addresses the need for clinical accuracy during test interpretation, especially in POC or at-home diagnostic tests, by developing an internal amplification control (IAC). Here, I develop a one-pot duplex reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) assay for detecting SARS-CoV- 2 along that incorporates a housekeeping gene as an IAC to ensure the quality of collected samples and the validity of assay reagents. The valid results can be easily visualized in triple-line lateral flow immunoassay (LFIA). The second aim makes progress towards overcoming the limited analytical sensitivity of existing rapid diagnostic tests for acute HIV infection screening. Here, I introduce a novel antibody-initiated LAMP assay targeting the HIV p24 capsid protein that combines LAMP sensitivity with the specificity of HIV p24 and its antibody. There are 3000 p24 capsid proteins present in the virion compared to only 2 viral RNA copies. In the assay, two DNA- conjugated antibody probes will each bind to p24 and their proximity will allow the DNA overlaps to generate a complete DNA target that acts as a trigger for the LAMP reaction. An LFIA is integrated into this design to enable simple result visualization. The third aim improves manufacturability and assembly of our existing nucleic acid detection platform by simplifying the platform components while maintaining the user-friendly sample-to-answer concept. Here, I validate material compatibility testing, assess chamber fabrication methods amenable to large-scale manufacturing, evaluate alternative heating units, and examine fluid flow control mechanisms of the redesigned wax valve. These combined aims demonstrate promising outcomes for practical implementation of molecular diagnostics to the POC.</p>

The COVID-19 pandemic, caused by SARS-CoV-2, has emerged as one of most significant health emergencies in recent history. SARS-CoV-2 has been characterized by the emergence of highly mutated variants that exhibit high transmissibility, virulence, and the capability of immune escape. The constantly evolving nature of the COVID-19 pandemic has underscored the necessity for a thorough comprehension of viral transmission dynamics, the effectiveness of novel monitoring techniques, and the determinants of health inequalities. This study explored several aspects of the pandemic, specifically emphasizing the emergence and dissemination of the Delta variant in Florida, the significance of environmental surveillance, and the factors associated with COVID-19 outcomes. Phylogenetic analysis using SARS-CoV-2 genome revealed that multiple independent introductions of the Delta variant fueled its spread within Florida. Further, we hypothesized that high-touch surface monitoring can be an alternative noninvasive approach to determine infection trend and detect variants. The study found high contamination rate on high-touch surfaces and the viral gene copy was positively correlated to the clinical cases in the university. Moreover, genome sequencing of environmental surface samples detected circulating and emerging variants. Additionally, spatial autocorrelation and regression analysis was conducted to investigate the relationship between county-level demographic, socioeconomic, and health-related factors and variation in COVID-19 cases, mortality, and case fatality rates. This study identified significant variations in COVID-19 outcomes across Florida counties, with factors such as age, obesity, rurality and importantly, vaccination rates playing key roles in explaining these disparities. Overall, this study emphasizes the importance of robust genomic surveillance for monitoring the emergence and spread of viral variants, the potential of environmental surface monitoring as a complementary public health tool, and the urgent need to address the underlying drivers of health disparities. These findings contribute to a more nuanced understanding of pandemic dynamics and inform data-driven strategies to mitigate the impact of future public health emergencies.

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Tang Lok Ming. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 86-87). / Abstracts in English and Chinese. / Chapter 1. --- Introduction --- p.1 / Chapter 2. --- Severe Acute Respiratory Syndrome (SARS) --- p.8 / Chapter 2.1 --- Nature of SARS --- p.8 / Chapter 2.2 --- Impacts of SARS --- p.9 / Chapter 2.3 --- Literature of SARS --- p.13 / Chapter 2.4 --- Evolution of SARS in Mainland China --- p.16 / Chapter 3. --- Event Study Methodology --- p.18 / Chapter 4. --- Data --- p.24 / Chapter 5. --- Results --- p.25 / Chapter 5.1 --- Hong Kong --- p.26 / Chapter 5.2 --- Mainland China --- p.31 / Chapter 6. --- Conclusion --- p.47 / Figures --- p.50 / Tables --- p.59 / Appendix --- p.64 / References --- p.86

This paper explores WHO’s response during the COVID-19 pandemic and compares it to its response during the SARS epidemic in 2003. This is done by examining the organization’s performance through a policy output approach and theoretical perspectives of effectiveness and performance theories. The policy output approach offers an operational model that suggests studying five variables of output applied to the policy documents published by the organization. The results show that WHO has increased its performance and productivity since SARS 2003 which might indicate that the effectiveness of the organization could have increased along with it. However, in order to ultimately establish effectiveness, external factors such as compliance of member states and domestic politics needs to be considered in future studies. This study contributes to the understanding of WHO’s performance in times of crisis and can be used as background for further research on effectiveness.

Sammanfattning Sedan sjukdomen Covid-19s uppdykande i början av 2020 har forskning pågått för att karaktärisera sjukdomen ur alla tänkbara vinklar för att på kortast möjliga tid bereda väg för ett fungerande botemedel. Effektiva läkemedel som kan minska risken för allvarligt sjuka patienter att avlida i sjukdomen behövs; många preparat har föreslagits och testats och i Sverige har hittills två läkemedel godkänts för Covid-19. Ett av dessa är kortikosteroiden dexametason som godkänts för Covid-19-patienter i behov av syrgas eller respirator. Syftet med detta arbete var att undersöka hur effektiv kortikosteroidbehandling av svårt sjuka Covid-19-patienter var i jämförelse med standardbehandling utan kortikosteroider. En litteratursökning gjordes i PubMed och i covid-nma efter randomiserade kliniska studier av kortikosteroider jämfört med standardbehandling till patienter med Covid-19. Ur resultatet som inkluderade 7 kontrollerade studier med 7784 svårt sjuka patienter från 11 länder och fem kontinenter, gjordes en sammanvägning av den primära utfallsvariabeln mortalitet 28 dagar efter randomisering varpå relativ risk (RR) räknades ut individuellt per studie och sammanvägt för alla studier. Analysen gjordes också med den mest dominanta studien borträknad. Vidare utforskades möjliga samband mellan sjukdomsgrad och effektstorlek, dels genom ett försök till metaregression av studiemortalitet och andningshjälpsnivå mot RR som var inkonklusivt, men också genom att leta efter speciellt sjuka undergrupper i studierna. 3 studier rapporterade mortalitet efter 28 dagar, 1 studie rapporterade mortalitet efter 21 dagar, 2 studier rapporterade död på sjukhus och en studie rapporterade död efter 15 dagar. Testade preparat var dexametason, hydrokortison och metylprednisolon. Av 2885 patienter som randomiserats till någon kortikosteroid, dog 739, medan det av de 4899 som randomiserats till standardbehandling dog 1347 patienter vilket gav en icke signifikant RR på 0,93 (95% CI 0,86–1,01). Vid borträkning av den största studien som bestod av relativt friskare patienter erhölls en starkare och signifikant effekt med RR 0,80 (95% CI 0,70–0,92) baserat på 257 av 781 döda i steroidgrupperna jämfört med 237av 578 döda i någon kontrollgrupp med standardbehandling. Resultatet var även i linje med analysen av olika sjuka undergrupper från största studien som visade bäst effekt hos de med invasiv mekanisk andningshjälp (absolut riskreduktion 12,1%) samt en icke signifikant försämring hos de friskaste patienterna utan syrgasbehov. Sammantaget tyder dessa resultat på att behandling av svårt sjuka Covid-19-patienter med kortikosteroider minskar mortaliteten efter 28 dagar. Dessutom ger studien en stark indikation på att bästa effekten fås om kortikosteroiderna ges till patienter där den systemiska inflammationen i lungorna nått en gasutbyteshämmande nivå / ABSTRACT Since the emergence of the new corona virus disease, Covid-19, much research effort has gone into characterising every possible angle of the disease to pave the way for a possible cure in the shortest possible time. Effective therapies are needed that will reduce the risk of dying for severely to critically ill Covid-19 patients. Many existing therapies have been suggested, tested and repurposed for the treatment of Covid-19 but so far only two drugs have been approved in Sweden for this indication, namely the antiviral drug remdesivir and the corticosteroid dexamethasone. Corticosteroids are both immunosuppressive and anti-inflammatory and when they were administered previously for severe acute respiratory syndrome (SARS), middle east respiratory syndrome (MERS) and influenza they were found to increase the time to rid the body of virus. The purpose of this study was to investigate evidence found in the research literature of how effective corticosteroids are in reducing the risk of dying as compared to standard treatment with no corticosteroids when administered to hospitalised patients with severe Covid-19. A literature search was made in the PubMed and covid-nma databases for randomized clinical studies of corticosteroids versus standard treatment to patients with Covid-19. The result included 7 studies with 7784 patients from 11 countries and 5 continents which all reported death as an outcome in groups that were receiving corticosteroids compared to groups that were receiving standard care. The studies used one of the following corticosteroids as intervention: dexamethasone, methylprednisolone and hydrocortisone in different doses. In the groups receiving standard care, 1347 patients out of 4899 died while in the corticosteroid groups 739 of 2885 patients died. When doing a statistical calculation these figures indicated that the risk of dying when getting corticosteroids was 93% of the risk when not getting corticosteroids, however the difference was not statistically significant. After omitting the largest study from the material, that contributed the absolute majority of total participants, who were deemed relatively healthy or well taken care of, the results were instead that 257 out of 781 died in the steroid groups and 237 of 578 died in the control groups. This later comparison among supposedly sicker patients, gave a statistically significant 8,1% lower absolute risk of dying in the corticosteroid groups; an effect that could also be expressed as for every 25 patients treated, 2 more lives would be saved. A further control of a more severely sick subgroup of patients from the largest study, in need of invasive mechanical ventilation, revealed an absolute reduction of the risk of dying when given corticosteroids of 12,1%. This group showed the most effectful response to the administered corticosteroids in this study which could also be expressed as 1 more life saved for every 8 patients treated. Another sub group analysis of the patients from the largest study that were not in need of any type of oxygen support, indicated on the other hand a possible harm of corticosteroids. This potentially harmful effect was however not statistically significant. In summary, the results of this study imply that administration of corticosteroids to patients with severe Covid-19 will reduce the risk of dying. The greatest effect is seen in those patients that has reached a level of illness were the gas exchange in the lungs is impaired by the inflammation. Furthermore, caution must be taken not to introduce harm by giving corticosteroids to patients with milder disease in which the immunosuppressive properties of the drug could lead to unintended worsening of the illness.

Introduktion: Sjukvårdspersonal runt om i världen har stått på frontlinjen i stressiga arbetsmiljöer och tagit hand om COVID-19-patienter sedan SARS-CoV-2 förklarades som en global pandemi. Under pandemiska förhållanden står sjukvårdspersonal inför specifika utmaningar, där vissa leder till symptom på psykisk ohälsa. Statliga resurser till sjukvårdspersonal har ofta avsatts för kortsiktiga insatser. Långsiktiga investeringar med fokus på främjande av sjukvårdpersonalens psykiska hälsa behövs för att förhindra förvärrade folkhälsoproblem på grund av SARS-CoV-2. Syfte: Studiens syfte var att belysa hur sjukvårdspersonal rapporterar att deras psykiska hälsa påverkats av SARS-CoV-2-pandemin och vilka erfarenheter från tidigare interventioner för psykisk hälsa som skulle kunna vara användbara för att förbättra sjukvårdspersonals psykiska hälsa genom att belysa några exempel. Metod: En systematisk litteraturöversikt genomfördes, där 20 vetenskapliga artiklar inkluderades och analyserades med tematisk analys. Resultat: Totalt nio teman identifierades: psykisk ohälsa hos sjukvårdspersonal, SARS-CoV-2-pandemin, interventioner för psykisk hälsa, vårdkvalitet, säkerhetskultur, arbetsplatsbaserade tillvägagångssätt, mindfulness och konstaktivitetsmetoder, biomarkörbaserade tillvägagångssätt samt tekniska tillvägagångssätt. Viktiga fynd i denna litteraturöversikt är att teman säkerhetskultur och vårdkvalitet är associerade med de andra teman. Slutsats: När tillvägagångssätt implementeras i insatser för sjukvårdspersonals psykiska hälsa som främjar säkerhetskultur och vårdkvalitet främjar det också, enligt resultaten i denna översikt, långsiktiga effekter på individuell psykisk hälsa hos sjukvårdspersonal. Detta bör omedelbart beaktas av dem som utvecklar nya program för att främja psykisk hälsa för att stödja sjukvårdspersonal i effekterna av pandemin. / Introduction: Healthcare workers around the world have stood on the front lines in stressful work-environments, caring for COVID-19 patients since SARS-CoV-2 was declared a global pandemic. Under pandemic conditions healthcare workers face specific challenges, where some lead to symptoms of mental illness. Governmental resources to the healthcare workforce have often been allocated to short-term efforts. Long-term investments focusing on mental health promotion for HCW are needed to prevent worsening public health issues due to SARS-CoV-2. Aim: The aim of the study was to illuminate how HCW report that their mental health has been affected by the SARS-CoV-2 pandemic and what experiences from previous mental health interventions that may be useful in promoting HCW mental health by highlighting some examples. Methods: A systematic literature review was conducted, including 20 scientific articles analyzed with thematic analysis. Results: A total of nine themes were identified: mental distress in HCW, SARS-CoV-2 pandemic, mental health interventions, quality of care, safety culture, workplace-based approaches, mindfulness and art activity approaches, biomarker-based approaches as well as technology approaches. Important findings in this literature review are the themes safety culture and quality of care being associated with the other themes. Conclusion: When implementing approaches in mental health interventions for HCW that promote safety culture and quality of care, it also promotes, according to the findings in this review, long-term effects in individual mental health in HCW. This should be urgently taken into consideration by those developing new mental health promotion programs to support HCW in the effects of the pandemic.

Coronavirus disease 2019 (covid-19) är en smittsam infektionssjukdom som orsakas av viruset severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sedan sjukdomens utbrott i december 2019 har viruset spridits globalt och infekterat fler än 270 miljoner människor världen över. Majoriteten av de som insjuknar i covid-19 får lindriga till måttliga besvär, men en liten del blir allvarligt sjuka och behöver sjukhusvård. Bland de patienter som blir allvarligt sjuka i covid-19 diagnostiseras en betydande del i det akuta skedet med sväljsvårigheter, eller dysfagi. Föreliggande studie bestod i en retrospektiv journalgranskning, som en del av ett kvalitetssäkringsarbete inom Region Gävleborg. Syftet med studien var att undersöka hur sväljsvårigheter kan manifesteras hos personer som vårdas på sjukhus till följd av covid-19 och som remitterats till logoped för bedömning och åtgärder. 60 deltagare inkluderades i studien, varav 17 var kvinnor och 43 var män. Resultaten visar att förekomsten av dysfagi var hög i det akuta skedet, där 42 deltagare (70 %) bedömdes ha dysfagi vid första logopedbedömning. Många deltagare återhämtade sig från sin dysfagi under vårdtiden, men 12 deltagare (20 %) hade kvarstående dysfagi vid utskrivning. Behovet av nutritionsstöd och andningsstöd under vårdtiden var stort. Vanliga fynd under de kliniska sväljbedömningarna var hosta, trögutlöst sväljning och nedsatt oral bearbetning. Deltagarna erhöll logopediska rekommendationer främst gällande anpassad kost, sittställning och munvård. Deltagarnas sväljförmåga skattades med Functional Oral Intake Scale (FOIS) vid första logopedbedömning och vid utskrivning. Vid första bedömning rekommenderades en majoritet av deltagarna anpassad kost (FOIS 1–6) och medelvärdet för FOIS var 3,5 ± 2,1. Vid utskrivning hade de flesta återgått till normalkost (FOIS 7) och medelvärdet för FOIS var 6,0 ± 1,8 (p &lt; 0,001). Denna studie visar att en majoritet av de som vårdats på sjukhus till följd av covid-19 i Region Gävleborg och som remitterats till logoped, uppvisade dysfagi i det akuta skedet men kunde vid utskrivning äta normalkost. Behovet av mer forskning och vidare analyser av hur sväljsvårigheter manifesteras och upplevs hos patientgruppen är fortsatt stort. / Coronavirus disease 2019 (COVID-19) is a contagious infectious disease caused by the virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since the outbreak in December of 2019, the virus has spread globally and infected more than 270 million people worldwide. The majority of people infected with COVID-19 will have mild to moderate symptoms, but some will suffer from severe illness which requires hospital care. Many of those who experience severe illness from COVID-19 are diagnosed with swallowing difficulties, or dysphagia, in the acute stage. This study consisted of a retrospective medical chart review and is part of a review of quality control in Region Gävleborg. The aim of the study was to investigate how swallowing difficulties manifest in people who require hospital care due to COVID-19 and who have been referred to the Speech and Language Therapy department. 60 participants were included in the study, of whom 17 were women and 43 were men. The results show that the prevalence of dysphagia was high in the acute stage, where 42 participants (70%) were diagnosed with dysphagia during the first SLT assessment. Many participants recovered from their dysphagia during their hospital stay, but 12 participants (20%) had persistent dysphagia at discharge. The need for nutritional and respiratory support was high. Common findings from the clinical swallowing assessments were coughing, difficulty initiating swallowing as well as affected oral processing. Common SLT recommendations included modified consistencies, posture and oral care. Swallowing ability was graded with the Functional Oral Intake Scale (FOIS) at first SLT assessment and at discharge. At first SLT assessment a majority of the participants were recommended a modified diet (FOIS 1-6) and the average FOIS was 3.5 ± 2.1. At discharge most participants had returned to a normal diet (FOIS 7) and the average FOIS was 6.0 ± 1.8 (p &lt; 0,001). This study shows that a majority of the people who were hospitalized due to COVID-19 in Region Gävleborg and who were referred for an SLT evaluation, had dysphagia in the acute stage and recovered from their swallowing difficulties before discharge. More research and further analyses of how swallowing difficulties manifest in patients hospitalized due to COVID-19 is still needed.