<b>Background</b>: The world is at risk of epidemics of novel and reemerging infectious diseases. These may be national, regional or international as in the case of Nipah, African Viral Haemorrhagic Fevers, SARS and H1N1 respectively. It is crucial that public health and clinical research is conducted in such epidemics. Yet the conduct of heath research during rapidly evolving epidemics or disasters represents an enormous challenge. In addition to the large number of practical challenges to undertaking such research there are also major ethical issues to consider. However, there is very little understanding of these ethical issues and very little empirical evidence of the views of patients, their families, society and key stakeholders. <b>Objective</b>: To collect and analyse data on ethical considerations arising in the setting of research on rapidly evolving epidemics posed by the urgent and unpredictable nature of epidemics. <b>Design</b>: The study was conducted in Oxford University Clinical Research Unit (OUCRU), Viet Nam and 3 other hospitals in Viet Nam with experience of epidemics. Data were collected by semi-structured interviews with key stakeholders representing research staff, IRB members, patients/family members and study sponsors/funders who have participated in or reviewed research projects on infectious diseases including SARS, H5N1, H1N1, dengue and Hand, Foot, Mouth disease. <b>Result</b>: A total of 64 interviews with all key stakeholders were conducted. Analysis of the ethical problems/challenges discussed in the interviews led to the identification of three themes 1) International research collaboration, 2) IRB review and 3) Consent. These tended to arise at three levels of relationship: macro (between institutions internationally), meso (within and between institutions nationally) and micro (within institutions and between health professionals and patients). <b>Conclusion</b>: The issues and types of considerations and their relative importance were raised and/or valued differently by the members of different key stakeholder groups due to their role and experience in research participation. Some of the issues raised also related to health research in other settings. However, many were unique to the setting of rapidly evolving epidemics. Addressing these issues is crucial for successful and appropriate research in the context of epidemics. It is inevitable that epidemics of emerging and reemerging infectious diseases will occur in the future and there is a clear need to undertake crucial scientific research in such settings. It is therefore imperative that we understand the challenges and ethical issues surrounding such research. It is desirable that further research into the ethical challenges identified in this thesis takes place in the inter-epidemic period in order to better prepare for the next epidemic.

Chlamydia trachomatis (CT) is a pestilent infection affecting upwards of 90 million people worldwide. An efficacious vaccine is needed to control the morbidities and rising healthcare cost associated with genital CT infection. We have established that protection against chlamydia infection parallels with a high frequency of T helper Type 1 cells and the associated antibodies. The current study focuses on the induction of innate immune responses involved during Chlamydia infection by a Vibrio cholera ghost-based (VCG) vaccine vector. THP-1 cells were used for dose and kinetic experiments. HeLa cells were used for infectivity assays. Based on preliminary studies, we hypothesized that the induction of immune responses by a VCG-based vaccine involves multiple innate immune signaling. Multiplex assay was used to measure T helper Type I and Type II cytokine secretion by THP-1 monocytes (Mn) or macrophages (Mϕ). Immunostimulatory cytokine secretion was significant when both cell morphologies were pulsed with VCG or VCG/murine splenocytes. We concluded that this secretion was significant enough to compliment that which would be secreted when THP-1 cells are pulsed with Chlamydia elementary bodies alone, enhancing the innate immune response during infection. Cellular supernatants (conditioned media) containing Th1-type and Th2-type cytokines were used to culture Chlamydia-infected HeLa cell monolayers. Infected HeLa monolayers cultured in the conditioned media were significantly less infected (968 IFUs) versus HeLa monolayers cultured in Earle’s minimum essential media (16,486 IFUs; p<0.001). We concluded that factors contained in conditioned media prevent and/or significantly reduce infection by Chlamydia and the development of inclusion forming units.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

Infectious disease management system area is considered as an emerging field of modern healthcare in the Gulf region. Significant technical and clinical progress and advanced technologies can be utilized to enhance the performance and ubiquity of such systems. Effective infectious disease management (IDM) can be achieved by analysing the disease management issues from the perspectives of healthcare personnel and patients. Hence, it is necessary to identify the needs and requirements of both healthcare personnel and patients for managing the infectious disease. The basic idea behind the proposed mobile IDM system in this thesis is to improve the healthcare processes in managing infectious diseases more effectively. For this purpose, internet and mobile technologies are integrated with social networking, mapping and IDM applications to improve the processes efficiency. Hence, the patients submit their health related data through their devices remotely using our application to our system database (so-called SAIF). The main objective of this PhD project was the design and development of a novel web based architecture of next-generation infectious disease management system embedding the concept of social networking tailored for Saudi patients. Following a detailed literature review which identifies the current status and potential impact of using infectious diseases management system in KSA, this thesis conducts a feasibility user perspective study for identifying the needs and the requirements of healthcare personnel and the patients for managing infectious diseases. Moreover, this thesis proposes a design and development of a novel architecture of next-generation web based infectious disease management system tailored for Saudi patients (i.e., called SAIF – infectious diseases management framework for Saudi Arabia). Further, this thesis introduces a usability study for the SAIF system to validate the acceptability of using mobile technologies amongst infected patient in KSA and Gulf region. The preliminary results of the study indicated general acceptance of the patients in using the system with higher usability rating in high affected patients. In general, the study concluded that the concept of SAIF system is considered acceptable tool in particularly with infected patients.

Mycobacterium tuberculosis (Mtb) causes human tuberculosis, and more people die of it than of any other pathogen in the world. Immunodominant antigens elicit the large majority of T cells during an infection, making them logical vaccine candidates. Yet, it is still unknown whether these immunodominant antigen-specific T cells recognize Mtb-infected cells. Two immunodominant antigens, TB10.4 and Ag85b, have been incorporated into vaccine strategies. Surprisingly, mice vaccinated with TB10.4 generate TB10.4-specific memory CD8+ T cells but do not lead to additional protection compared to unvaccinated mice during TB. Ag85b-specific CD4+ T cells are also generated during vaccination, but the literature on whether these cells recognize Mtb-infected cells is also inconsistent. We demonstrate that TB10.4-specific CD8+ T cells do not recognize Mtb-infected cells. However, under the same conditions, Ag85b-specific CD4+ T cells recognize Mtb-infected macrophages and inhibit bacterial growth. In contrast, polyclonal CD4+ and CD8+ T cells from the lungs of infected mice can specifically recognize Mtb-infected macrophages, suggesting macrophages present antigens other than the immunodominant TB10.4. The antigen location may also be critical for presentation to CD8+ T cells, and live Mtb may inhibit antigen presentation of TB10.4. Finally, we propose that TB10.4 is a decoy antigen as it elicits a robust CD8+ T cell response that poorly recognizes Mtb-infected macrophages, allowing Mtb to evade host immunity.

Masks have become an important part of everyday life, protecting both the wearer and individuals nearby from the spread of infectious diseases, most notably severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the coronavirus that causes coronavirus disease 2019 (COVID-19). However, these masks are easily contaminated, whether through continued use or by the wearer touching the mask fabric with contaminated hands, therefore reducing the efficacy and exposing the user to these contagions. When the mask becomes contaminated, it can be discarded, which produces large amounts of waste that will end up in a landfill, or it can be washed, which is costly, wasteful, and time consuming. Our solution to this problem is a mask apparatus that can sanitize itself quickly on demand. The user wears the shell, which contains the fully retracted mask, on a string like they would a necklace. When the mask is required, it is easily pulled out of the shell and can be worn for as long as the user needs it. When it is safe to remove the mask, the user simply pushes a button and the mask retracts back into the shell, where it is then sanitized for the next use. The design of the apparatus features a retractable cloth mask that is sanitized using ultraviolet-C (UVC) radiation while confined safely within an outer shell, minimizing unwanted exposure to the wearer. UVC radiation at wavelength 222 nm has been shown to destroy the outer shell of coronaviruses similar to SARS-CoV-2, inactivating 99.9% of the virus when exposed at a dosage of 2 mJ/cm2. The 28 light-emitting diode (LED) lamps used in this prototype produce this specified wavelength UVC and are separated into 4 strips located in different locations within the shell. Glass rods were used within the shell to guide the mask fabric into a zig-zag shape when fully retracted to maximize exposure to the UVC. To further reduce waste, two lithium-ion rechargeable batteries were used as the power supply for the lamps. The efficacy of this design for inactivating the SARS-CoV-2 coronavirus on the mask was determined indirectly using nano membrane UV sensors placed on the mask fabric, showing that the specified wavelength of UVC radiation can be applied for the required time on all surfaces of the mask. This mask apparatus can directly benefit both front-line healthcare workers as well as individuals going about their daily lives by eliminating pathogens present on their masks, therefore reducing the spread of deadly infectious diseases.

In 1989 the hepatitis C virus was identified as a significant cause of post-transfusion hepatitis. Nearly two decades later there is still no vaccine, inadequate treatment options, and limited understanding of how the virus establishes chronicity in the majority of the people it infects. Recent reports suggest that the interaction of a negative co-stimulatory pathway mediated by PD-1 and PDL-1 is associated with persistent viral infection. The role, if any, that PD-1/PDL-1 has in HCV infection is unknown. In this study we report that PD-1 is upregulated in T-cells from persons with chronic HCV infection when compared to healthy donors. In addition, PD-1 and PDL-1 are upregulated on T-cells from healthy donors when exposed to extracellular HCV core protein (a nucleocapsid protein that is immunosuppressive); upregulation of PD-1 is mediated by core's ability to bind to the complement receptor gC1q. We also report that the observed T-cell function can be restored by blocking the PD-1/PDL-1 interaction. Our results indicate that HCV core can upregulate an important negative T-cell signaling pathway that is associated with viral persistence. This upregulation of PD-1/PDL-1 represents a novel and perhaps shared mechanism that viral pathogens may use to subvert the human immune response. It also represents a potential new treatment option for the millions of people who suffer from chronic hepatitis C infection.

Human immunodeficiency virus (HIV) has become a global pandemic over the past few decades, with new infections and related deaths in the millions each year. There is no cure in sight for HIV-1 infection, and there has been little progress in developing an efficacious vaccine. Heterosexual transmission of HIV-1 remains the principal mode of transmission throughout the world and thus measures, such as topical vaginal microbicides, to prevent infection of the female reproductive tract are actively being explored. Recent trials of topical vaginal microbicides have shown that their interaction with the mucosal surfaces of the female reproductive tract as well as semen can hinder microbicide effectiveness against HIV-1 infection. Therefore, understanding the role these fluids play in HIV transmission would be critical towards developing effective antiviral prophylaxes. A recent study from our group demonstrated that human cervicovaginal secretions contained numerous cationic antimicrobial peptides and proteins, which collectively inhibited HIV-1 infection of target cells and tissues. To ascertain if human seminal plasma (SP), the main vector responsible for transmitting HIV-1, exhibited antiviral activity we utilized several antiHIV assays in the presence or absence of minimally manipulated SP. The majority of the intrinsic anti-HIV-1 activity of SP resided in the cationic polypeptide fraction. Antiviral assays utilizing luciferase reporter cells and lymphocytic cells revealed the ability of whole SP to prevent HIV-1 infection, even when SP was diluted 3200-fold. Subsequent fractionation by continuous flow acid-urea (AU)-PAGE and antiviral testing revealed that cationic polypeptides within SP were responsible for the majority of anti-HIV-1 activity. A proteomic approach was utilized to resolve and identify 52 individual cationic polypeptides that contribute to the aggregate anti-HIV-1 activity of SP. One peptide fragment of semenogelin I, termed SG-1, was purified from SP by a multi-step chromatographic approach, protein sequenced, and determined to exhibit anti-HIV-1 activity against HIV-1. Anti-HIV-1 activity was transient, as whole SP incubated for prolonged time intervals exhibited a proportional decrease in anti-HIV-1 activity that was directly attributed to the degradation of semenogelin I peptides. Collectively, these results indicate that the cationic polypeptide fraction of SP is active against HIV-1, and that semenogelin-derived peptides contribute to the intrinsic anti-HIV-1 activity of SP. Conversely, naturally occurring peptidic fragments from the SP-derived prostatic acid phosphatase (PAP) have been reported to form amyloid fibrils called "SEVI" capable of enhancing HIV-1 infection in vitro. In order to understand the biological consequence of this proviral effect, we extended these studies in the presence of human SP. PAP-derived peptides were agitated to form SEVI and incubated in the presence or absence of SP. While PAP-derived peptides and SEVI alone were proviral, the presence of 1% SP ablated their proviral activity in several different anti-HIV-1 assays. The anti-HIV-1 activity of SP was concentration dependent and was reduced following filtration. Supraphysiological concentrations of PAP peptides and SEVI incubated with diluted SP were degraded within hours, with SP exhibiting proteolytic activity at dilutions as high as 1:200. Sub-physiological concentrations of two prominent proteases of SP, prostate-specific antigen (PSA) and matriptase, could degrade physiological and supraphysiological concentrations of PAP peptides and SEVI. While human SP is a complex biological fluid, containing both antiviral and proviral factors, our results suggest that PAP peptides and SEVI may be subject to naturally occurring proteolytic components capable of reducing their proviral activity. Our studies demonstrate the overall antiviral activity of human SP, but there is still a critical need for effective topical vaginal microbicides that can prevent HIV-1 transmission. The synthetic human retrocyclins are cyclic antimicrobial peptides that are remarkably active against HIV-1, and are being developed as topical vaginal microbicides. Herein, we assessed whether the putative proviral SEVI was able to adversely affect the anti-HIV-1 activity of the retrocyclin analog RC-101. While SEVI alone enhanced viral infection, this effect was completely negated in the presence of RC-101. Retrocyclins such as RC-101 are inhibitors of HIV-1 entry, by preventing gp41-mediated viral fusion. Interestingly, using an HIV-1 reverse transcriptase (RT) specific assay, we also determined that RC-101 directly inhibited the activity of RT in a dose dependent manner, suggesting a secondary mechanism of viral inhibition. Our group has determined that RC-101 induces only a modest level of resistance in HIV, which may be due in part to RC-101's dual mechanisms of viral inhibition.

<p>Antibiotic use is generally regarded as the major driver for resistance. Many studies reporting an association between antibiotic use and the emergence of resistance have been published. However, most studies have significant limitations such as single center data with comparably low number of cases, using retrospective designs with limited data availability, ecological studies with lack of assessing the individual level and risk for ecological fallacy, and inappropriate selection of controls in case-control studies.</p> <p>A cohort study in adult patients hospitalized in 15 participating acute care hospital sites in Ontario, Canada, was conducted from April 1 2005 to June 30 2006. Antibiotic use on the unit level in defined daily doses (DDD) was only available for 3 sites. In order to assess antibiotic use on both the individual as well as on the unit level as a risk factor for resistance, days of therapy (DOT) could be calculated. However, it was unclear whether this approach would results in similar findings as when using DDD. Thus, the impact of using either DDD or DOT on the risk estimates for resistance was assessed for three antimicrobial-bacteria combinations, i.e. fluoroquinolone use and fluoroquinolone resistance in enterobacteriaceae an in <em>Pseudomonas aeruginosa</em>, and the use of betalactams and resistance to third generation cephalosporins in enterobacteriaceae.</p> <p>The risk estimates for resistance were very similar for all three antimicrobial-bacteria combinations on acute care units, there were some discrepancies on the unit level on intensive care units, and discrepancies on both levels for step down and rehabilitation units.</p> <p>In conclusion, the approach to use DOT instead of DDD to measure antibiotic utilization revealed similar results. However, the lack of comprehensive information on patient transfers when calculating DOT may bias the findings on units with frequent patient transfers such as intensive care units and step down and rehabilitation units.</p> / Master of Science (MSc)

<p>Majority of new HIV-1 infections world-wide occur via the genital tract. Therefore, achieving effective mucosal immunity will be a critical component of vaccine strategies in the prevention and control of infection during early stages of transmission itself. Rigorous efforts have been made to identify conserved epitopes and develop rational design of immunogens, in order to elicit broadly-reactive protective Abs against HIV. Newly emerging data have highlighted the significance of Ab effector functions other than classical IgG-mediated neutralization in HIV infection. In the studies contributing towards this thesis, an optimized vaccine model is described that successfully elicits potent systemic and mucosal Abs against the highly conserved epitopes of the membrane-proximal external region and the coiled coil region of gp41. Intriguing observations are reported on the IgA-inducing capacity of the coiled coil epitope, QARVLAVERY, which highlight the potential of this epitope as an attractive candidate for mucosal vaccines. Most importantly, the epitope-specific Abs proved to be functional in neutralizing HIV in a standardized assay. With particular relevance to mucosal protection, epitope-specific IgA also effectively inhibited the transcytosis of HIV in an optimized transwell assay. The effect of gp41-specific Abs was also assessed against a novel panel of HIV-1 viral clones, and exhibited significant protection. These clones selectively express envelopes from viruses that would be desired targets of prophylactic immune responses, the earliest founder population in the mucosa after virus transmission.</p> / Doctor of Philosophy (PhD)