Despite the existence of a treatment, there is still not a cure for HIV-1 infection and there arearound 700 000 deaths per year from AIDS-related diseases. A major barrier for a cure is theestablishment of latent reservoirs that are impossible to distinguish from healthy cells and thuscan escape the immune system. One potential solution is called shock-and-kill strategy, whichaims to induce HIV-1 reactivation, exposing latently infected cells to the immune system andmaking them susceptible to cell death. In our lab, it was seen that when NK cells are stimulatedwith a pan-caspase inhibitor, they acquire the “shock” ability, but it is still unknown how. Inthis project, we observed that the supernatant from pan-caspase inhibitor-stimulated NK cellscan increase HIV-1 reactivation in two different latency models. Furthermore, the protein levelsof three HIV-1 suppressors were found to be increased in the same supernatant. For this reason,their effect in HIV-1 reactivation in latently infected cells was analysed. Although we did notobserve an increase in HIV-1 reactivation, the upregulation of these three proteins can be usefulin the clinical context. Since they are HIV-1 suppressors, their presence can prevent theinfection from spreading after latent cells are reactivated. Altogether, our results show that NKcells stimulated with a pan-caspase inhibitor are secreting a biological product that inducesHIV-1 reactivation. This indicates that there is a pathway in NK cells that can potentially beexploited in order for them to be able to induce HIV-1 reactivation.

To end the HIV epidemic, prevention of new HIV infections will be contingent on preventing at-risk individuals from acquiring HIV and supporting people living with HIV in achieving and sustaining viral suppression throughout their lifetime. The underlying motivation for this dissertation is the recent evidence that new HIV infections can be prevented when people living with HIV achieve and maintain viral suppression. In response, three studies were conducted. The goal of this dissertation was to advance our understanding of HIV viral suppression patterns over time among clinically engaged adults living with HIV and examine current limitations in viral suppression monitoring. First, a systematic review evaluated the existing literature for evidence of longitudinal assessments of viral suppression among people living with HIV. Among 896 publications identified during the database search, 50 publications met the study criteria and were included in the review. Among these studies, 78% were implemented in the United States, 72% assessed viral suppression using viral load results abstracted from clinical medical records, and 22% used surveillance data from HIV-laboratory based reporting. Five distinct longitudinal measurement methods were identified, including (a) estimates requiring more than one viral load within an observation period to be below a suppression threshold; (b) estimates comparing the first and last viral load during an observation period; (c) reporting multiple proportions of participants maintaining viral suppression across an observation period; (d) estimating viremia copy-years and estimating person-time above a suppression threshold, and; (e) other methodology to assess longitudinal viral suppression such as data weighting and group-based trajectory modeling. Half of the studies reported the proportion of individuals with all viral loads below a certain threshold (e.g., ≤200 copies/mL). Most studies (70.0%; 35/50) were published in the last five years (2015 – 2019) and describe viral load data collected between 2013 and 2018, highlighting recent efforts by researchers to describe viral suppression using longitudinal approaches. Next, data from a longitudinal electronic medical record-based prospective cohort study of people living with HIV seeking care in Washington, District of Columbia, were used to describe longitudinal changes in viral suppression and assess the relationship between prior virologic history and virologic failure events during follow-up. Among 3556 participants, 29% did not maintain viral suppression during a five-year period, and instances of viral suppression status fluctuations were observed. Participants with a history of fluctuating viral suppression were found to have a higher rate (RR=2.40; 95% CI: 2.03 – 2.84; P<0.01) of virologic failure events during follow-up, compared to participants with sustained viral suppression before the observation period. Lastly, a third study used the same data source to assess differences between viral suppression estimates derived from different measurement methods and evaluate the impact of data triangulation on longitudinal viral suppression measures. Among 3452 participants (median age 48; 73% cisgender males; 77% non-Hispanic black), 69% had all viral load results suppressed (<200 copies/mL) during a four-year observation period, 28% had both suppressed and unsuppressed viral loads, and 2% had all viral loads unsuppressed. Compared to cross-sectional viral suppression measurement methods, longitudinal measurement methods resulted in lower proportions of virally suppressed participants. Data triangulation added 2293 viral load data points and resulted in lower viral suppression estimates. These findings highlight the need to reconsider current viral suppression measurement methods to improve the accuracy of estimates reported in surveillance reports and epidemiologic studies. Overall, this dissertation addresses important questions related to viral suppression by describing the frequency of viral suppression status fluctuations that occur throughout an extended observation period, quantifying the occurrence of repeated virologic failure events, and comparing several measurement techniques to assess appropriate methods to describe viral suppression over time. Recently, the United States Department of Health and Human Services, together with the White House, set forth the “Ending the HIV Epidemic: A Plan for America” initiative, with a goal to end the HIV epidemic in the United States within the next ten years. To reach this goal, the initiative calls for a 75% reduction in new HIV infections by 2025 and a 90% reduction by 2030. Treating people living with HIV rapidly and effectively with ART is an important strategy to carry out these efforts. This dissertation demonstrates that assessing the ability of people living with HIV to maintain viral suppression over time is also critical.

Includes bibliographical references (leaves 81-85). / HIV and AIDS are still affecting many people in Brazil, South Africa and across the world, even though much has been done to mitigate against its further spread. Often Brazil and South Africa are compared to each other because of their economic position in the world and also because of their similar political histories. This research compares the Brazilian and the South African HIV and AIDS National Strategic prevention policies and it also aims to find out why the HIV and AIDS prevalence rates took significantly different patterns in the respective countries. The study includes a policy comparison and qualitative in-depth interviews with 14 organisation directors whose main focus is HIV prevention in Brazil and South Africa. The mains findings revealed that one of the main reasons for the different prevalence rate in both countries was because the civil society in Brazil played a major role in pressurizing the government to respond to the pandemic, while in South African the civil society did not play a major role. The Brazilian government thus started responding to HIV at least 9 years before the South African government did. Also, the Brazilian National HIV and AIDS prevention policy has an action plan for each goal, while the South African Policy does not have action plans for their goals. The Brazilian policy is also decentralized to municipal level, while the South African policy is decentralized only to Provincial level. Another finding was that in Brazil the NGO sector was directly involved in formulating the policy while in South Africa the NGO sector was not. In Brazil the respondents had a good knowledge and understanding of the policy, while in South Africa the respondents did not have a good knowledge of the policy. In Brazil NGOs have formed partnerships between themselves in order to deliver better services and to make their voices stronger when pressurising the government. Respondents in Brazil also knew what other organisations were doing. In South Africa organisations did not know what other organisations were doing and the NGOs did not have strong partnerships between themselves.

Background: HIV transmission is greatly reduced when antiretroviral treatment (ART) suppresses an infected person’s HIV viral load. It is unclear, however, whether the contextual risk of incident HIV is optimally reduced by widespread individual-level suppression of HIV viral load alone or in combination with other HIV prevention services. HIV service coverage and community norms can influence risk in small area geographies; and contextual factors, like gender inequality and stigma, may foster environments conducive to HIV transmission. Yet, the relationship between places with high HIV levels and the clustering of area risk factors is unknown. The goal of this dissertation is to learn if and how a geographically focused combination implementation strategy could reduce population-level HIV risk. Analyses explored whether small area risk profiles explain area differences in HIV. The guiding hypothesis is that in high HIV prevalence settings, low HIV service uptake in a geographically defined area increases the prevalence of high HIV viremia, leading to greater HIV transmission and incident HIV. Methods: A systematic review was conducted to examine the association between population-level measures of HIV viral load and incident HIV infection in generalized and concentrated epidemics. Publications were English, peer-reviewed articles published from January 1, 1995 through February 15, 2019 that explicitly defined HIV viral load and assessed outcomes of HIV recency, incidence, seroconversion, or new diagnosis. Studies sampled general or key populations through population-based surveillance registries, household-based enumeration, cluster sampling, or respondent driven sampling. Descriptive statistics summarized review findings. The Swaziland HIV Incidence Measurement Survey (SHIMS) data were used for the remaining analyses. Using a two-stage cluster-based design, a nationally representative, household-based sample of adults, ages 18-49 years was enrolled from December 2010 to June 2011 in Eswatini. Consenting adults completed an interview and received home-based rapid HIV testing and counseling. All seropositive samples were tested for HIV viral load using the COBAS AmpliPrep/Taqman HIV-1 Test, v 2.0. Adults testing HIV-seronegative were enrolled in a prospective cohort for the direct observation of HIV seroconversion, completing an interview and home-based rapid HIV testing six months later. Multi-level latent class modeling was performed to identify statistically significant combinations of HIV risk factors and to classify the combinations into small area risk profiles. In the cross-sectional sample, linear regression with robust standard errors assessed the correlation between area profiles and places with high levels of uncontrolled HIV infection, or HIV core areas, measured by the area prevalence of detectable virus (≥20 copies/milliliter) among HIV-positive adults and among all adults, regardless of HIV status. In the prospective cohort, generalized linear regression of longitudinal data assessed the association between area profiles and places prone to new HIV infections (i.e., HIV susceptible areas), measured by area-level HIV seroconversions. Results: The systematic review found an evidence base primarily of lower quality studies and inconsistent HIV viral exposure measurement. Overall findings supported a relationship between increasing levels of suppressed HIV in HIV-infected populations and fewer new infections over time. Better quality studies consistently showed higher population viremia (i.e. HIV viral quantity among all persons, regardless of HIV status) associated with HIV incidence in high prevalence populations; population viral load (i.e., HIV viral quantity among only HIV-positive persons) did not show an association with incident HIV in high prevalence, general populations and was inconsistent in key populations. To determine whether area risk profiles can pinpoint HIV core areas, latent class modeling was used to categorize 18,172 adults into one of six HIV risk types. The risk typology, classified through unique combinations of HIV service uptake and sexual risk behaviors, conveyed an adult’s propensity for HIV transmission and/or acquisition risk. The model next identified the area-level composite prevalences of HIV risk types; estimated the three most frequent, unique composite combinations; and categorized them into area risk profiles characterizing HIV risk: low-moderate acquisition risk, moderate acquisition/transmission risk, and high acquisition/transmission risk. The high acquisition/transmission areas comprised the largest proportions of highest risk transmission and acquisition types. The prevalence of detectable viremia progressively increased from low-moderate acquisition, moderate acquisition/transmission, and high acquisition/transmission profiles [17.7%, 25.4%, and 35.1%, respectively]. When compared with low-moderate acquisition areas, the prevalence of detectable viremia was 7.4% [p<.001] higher in moderate acquisition/transmission areas and 17.1% [p<.001] higher in high acquisition/transmission areas. The prevalence of detectable viral load significantly decreased from low-moderate acquisition to moderate acquisition/transmission areas [76.6% versus 68.7%, p<.001], and was significantly higher in high acquisition/transmission areas by 7.3% [p<.001], when compared with low-moderate acquisition areas. To determine whether area risk profiles can predict HIV susceptible areas, a total of 18,172 adults were surveyed of which 4396 [24%] had detectable viremia. 11,880 [96%; n=12,357] HIV-seronegative adults enrolled in the prospective cohort and 11,155 [94%] of them completed an endline visit. Four area profiles were identified, defined by unique patterns in prevalence of HIV viremia and of sexual risk behaviors. The proportion of HIV susceptible areas progressively increased from Profiles A, B, C, and D [14.3%, 21.8%, 24.6%, and 30.8%, respectively]. HIV susceptible areas were more than twice as likely to occur in Profile D than Profile A environments [RR 2.13, 95% confidence interval (CI) (1.13, 4.00); p=0.02]. Profile D areas had prevalences of unknown partner HIV status and detectable viremia at 28% and 24%, respectively. In contrast, Profile A areas had prevalences of only 8% with unknown HIV status and 31% with detectable viremia. Conclusion: This dissertation shows that geographic risk profiles can explain differences in population-level HIV outcomes. Risk factors spatially cluster in predictable, meaningful combinations that can inform an area typology of HIV risk. The co-location of adults predisposed to greater HIV risk may heighten levels of uncontrolled HIV infection, thereby creating potential area sources of ongoing transmission; however, the concurrent levels of other risk factors may have more influence in reducing population-level incidence than previously considered. A composite indicator of contextual HIV risk may reveal places core to HIV transmission and susceptible to HIV acquisition. Such area profiles may help identify the combination of locally specific risk factors that readily promulgate HIV and better inform the design of place-based HIV intervention packages to enhance current strategies towards global HIV control.

Dissertation submitted in partial fulfillment of the requirements for the Degree Master of Arts in Counselling Psychology at the University of Zululand, South Africa, 2003. / The study investigated student behaviour and knowledge related to HIV/AiDS on the University of Zuluiand campus. Because of the social and economic conditions that exist in the country today such research is seen as both urgent and pertinent it is hoped that the study will add to the knowledge base generated by other studies conducted at tertiary institutions throughout South Africa. The study had certain assumptions, which have been supported by the results of the survey, it was postulated that women students wouid be more conservative in sexual behaviour than mate students and that femaies would be more accepting and empathetic towards People living with HiV/AIDS (PLWHA). The study also predicted that there wouid be a segment of the student population who would reveal a dissonance between attitudes, knowledge and behaviours and also that a proportion of students of both sexes would reveal significant gaps in their knowledge about how HIV/AIDS is transmitted. These predictions are underpinned by the results and discussion thereof, which places them within the context of early 21st century South African society.

A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 28 May 2018. / Since their discovery, protease inhibitors continue to be an essential component of antiretroviral treatment for human immunodeficiency virus type 1 (HIV-1). However, the development of resistance to protease inhibitors remains one of the most significant challenges in the fight for sustained viral suppression in those infected with HIV-1. Studies show that specific mutations arising within the HIV-1 gag and protease genes can lead to the development of resistance. In this research, a South African HIV-1 subtype C Gag-protease variant (W1201i) was investigated. This variant was considered due to the presence of a mutation and insertion (N37T↑V), located within the hinge region of the protease enzyme. Moreover, the variant displayed the following polymorphisms: Q7K, I13V, G16E, M36T, D60E, Q61E, I62V and M89L. Genotyping of W1201i Gag revealed a previously unreported MSQAG insertion between the CA/p2 and p2/NC cleavage sites. Additionally, a mutation and insertion (I372L↑M), and multiple polymorphisms (S369N, S371N, I373M and G377S) were discovered within the p2/NC cleavage site. Single-cycle phenotypic assays were performed to determine the drug susceptibility and replication capacity of the variant. The results show that the mutations present in the N37T↑V protease conferred a replicative advantage and reduced susceptibility to lopinavir, atazanavir and darunavir. Interestingly, the mutations in W1201i Gag were found to modulate both replication capacity and protease inhibitor susceptibility. In silico studies were performed to understand the physical basis for the observed variations. Molecular dynamics simulations showed that the N37T↑V protease displayed altered dynamics around the hinge and flap region and highlighted the amino acids responsible for the observed fluctuations. Furthermore, induced fit docking experiments showed that the variant bound the iv protease inhibitors with fewer favourable chemical interactions than the wild-type protease. Collectively, these data elucidate the biophysical basis for the selection of hinge region mutations and insertions by the HI virus and show that protease, as well as Gag, needs to be evaluated during resistance testing. / EM2018

Indiana University-Purdue University Indianapolis (IUPUI) / More than 20 million people have died of AIDS since the early eighties, while nearly 34 millions are currently infected with the HIV. Anti-retroviral therapy (ART) directed at key viral enzymes has changed AIDS from uniformly fatal to a manageable chronic disease. However, ART-associated drug resistance and toxicity have posed a great challenge for long-term management of the disease and have called for development of new therapeutics. In this study, we focused on the viral factor Nef and the host factor Sam68. Nef is a major pathogenic viral determinant for HIV-1, and no therapeutics have been targeted to this factor. Sam68 is indispensible for HIV-1 propagation. We revealed that Sam68 variants were very potent in preventing Nef expression. We found that these effects were associated with their ability to form a macromolecular structure called stress granules (SG). In addition, we demonstrated that these variants bound to nef mRNA in a sequence-specific manner. Furthermore, we showed that these variants co-localized with nef mRNA in SG. Importantly, we validated these findings in the context of HIV-1 infection of its natural target cells and found significant loss of Nef function in these cells. Taken together, these results demonstrate that SG induction and nef mRNA sequestration account for translational suppression of Nef expression and offer a new strategy for development of anti-HIV therapeutics. Sam68 is implicated in a variety of other important cellular processes. Our findings that Sam68 variants were able to induce SG formation prompted us to investigate whether wild-type Sam68 was also recruited to SG. We found that Sam68 was increasingly recruited into SG under oxidative stress, and that its specific domains were involved. However, Sam68 knockdown had no effects on SG assembly, suggesting that Sam68 is not a constitutive component of SG assembly. Lastly, we demonstrated that Sam68 complexed with TIA-1, an essential SG component. Taken together, these results provide direct evidence for the first time that Sam68 is recruited into SG through complexing with TIA-1, and suggest that SG recruitment of Sam68 and ensuing changes in Sam68 physiological functions are part of the host response to external stressful conditions.

Indiana University-Purdue University Indianapolis (IUPUI) / Background: The current treatment for HIV/AIDS is called highly active antiretroviral therapy (HAART) and is a combination of anti-HIV reverse transcriptase inhibitors and protease inhibitors. HAART is capable of suppressing HIV replication and subsequently improving the patients’ survival. However, the issues associated with use of HARRT such as the high cost, severe side-effects, and drug resistance have called for development of alternative anti-HIV therapeutic strategies. In this study, we screened several traditional Chinese medicinal herbal extracts for their anti-HIV activities and determined their anti-HIV mechanisms. Methods: Nine traditional Chinese medicinal (TCM) herbal plants and their respective parts derived from Hainan Island, China were extracted using a series of organic solvents, vacuum dried, and dissolved in dimethyl sulfoxide. Initial anti-HIV activity and cytotoxicity of these extracts were evaluated in HIV-infected human CD4+ T lymphocytes Jurkat. Extracts of higher anti-HIV activities and lower cytotoxicity were selected from the initial screening, and further examined for their effects on HIV-1 entry, post-entry, reverse transcriptase, gene transcription and expression using combined virology, cell biology and biochemistry techniques. Results: Four extracts derived from two different herbal plants completely blocked HIV-1 replication and showed little cytotoxicity at a concentration of 10 g/ml. None of these four extracts had any inhibitory effects on HIV-1 long terminal repeat promoter. Two of them exhibited direct inhibitory activity against HIV-1 reverse transcriptase (RT). All four extracts showed significant blocking of HIV-1 entry into target cells. Conclusions: These results demonstrated that four TCM extracts were capable of preventing HIV-1 infection and replication by blocking viral entry and/or directly inhibiting the RT activity. These results suggest the possibility of developing these extracts as potential anti-HIV therapeutic agents.

This study was conducted to determine retention rate and factors associated with loss to follow-up (LTFU) of adult pre-ART patients in St. Luke hospital, Ethiopia. Cross-sectional study with quantitative and qualitative data collection techniques was used. Review of patient records, focus group discussions and review of program guidelines was conducted to determine level of adherence among pre-ART patients. In addition, pre-ART service quality and perceived reasons for discontinuation was explored. The study revealed that only 38.2% of the 335 patients enrolled in the pre-ART care were retained after 12 months of follow-up in the program. More than half (55.6%), of the LTFU occurred during the first 6 months of follow-up. Fear of discrimination, high transportation cost and mistrust in the pre-ART service were perceived reasons for LTFU. Absences of clear pre-ART service package and implementation guideline were also identified as important factors that may be related to LTFU. The findings call for improved quality of care and a better pre-ART service packaging that will address the gaps identified in order to increase patient retention. / Health Studies / MA (Public Health)

This study was conducted to determine retention rate and factors associated with loss to follow-up (LTFU) of adult pre-ART patients in St. Luke hospital, Ethiopia. Cross-sectional study with quantitative and qualitative data collection techniques was used. Review of patient records, focus group discussions and review of program guidelines was conducted to determine level of adherence among pre-ART patients. In addition, pre-ART service quality and perceived reasons for discontinuation was explored. The study revealed that only 38.2% of the 335 patients enrolled in the pre-ART care were retained after 12 months of follow-up in the program. More than half (55.6%), of the LTFU occurred during the first 6 months of follow-up. Fear of discrimination, high transportation cost and mistrust in the pre-ART service were perceived reasons for LTFU. Absences of clear pre-ART service package and implementation guideline were also identified as important factors that may be related to LTFU. The findings call for improved quality of care and a better pre-ART service packaging that will address the gaps identified in order to increase patient retention. / Health Studies / MA (Public Health)