Rebound Relationships: An Investigation Of Hiv-1 Rebound Dynamics And Host Immune Responses During Analytical Treatment Interruption

In HIV-infected patients, combination antiretroviral therapy (cART) during HIV-1 infection potently suppresses viral replication and slows progression to AIDS. Upon cessation of cART, however, systemic infection is rapidly re-established due to the long-lived pool of latently infected cells, or HIV reservoir, that is seeded early in infection and persists despite years of cART in patients. This long-lived reservoir is the target of novel curative strategies. In order to determine in vivo efficacy of these interventions, closely monitored analytical treatment interruption (ATI) is required. Previously conducted ATI trials have provided important baseline information regarding the kinetics and diversity of viruses emerging from latency. As future HIV curative clinical trials move towards prolonged periods of ATI, studies assessing the effect of ATI on host virus-immune dynamics will provide an important baseline that will further our understanding of trial outcomes. In this thesis, I conducted single genome sequencing (SGS) of HIV-1 env and neutralization assays using autologous antibodies to characterize the viral and immune dynamics of rebound in two clinical trials: a longitudinal ATI study in the absence of any intervention, and a brief ATI study involving administration of the broadly neutralizing antibody VRC01. Our data, consistent with previous studies, demonstrated that viral rebound occurs within four weeks of ATI and is established by multiple latently infected cells in the majority of HIV-infected participants. Analyses of plasma containing VRC01 and/or autologous antibodies show that latent reservoir viruses can experience an antibody-mediated neutralization sieve effect, thus preventing the persistence of antibody-sensitive viruses. Additionally, SGS of latent viruses before and after brief ATI show that the size and composition of the peripheral latent viral reservoir is not significantly altered during ATI, demonstrating that short-term ATI is safe. Taken together, these data highlight the complex virus-host dynamics during ATI, and further suggest that passively infused or host-derived neutralizing antibodies can exert selective pressure, altering the evolution of HIV in its host

Characterizing the neurological impact of acute HIV infection and its outcomes after immediate initiation of antiretroviral therapy

HIV invades the central nervous system (CNS) during early infection and contributes to neurocognitive impairment during chronic infection. This thesis aims to investigate the neurological impact of acute HIV infection (AHI) and its outcomes after immediate initiation of antiretroviral therapy (ART). Section 1 of this thesis is an introduction to the persistence of HIV-associated neurocognitive disorder in the ART era, highlighting the need to study AHI to understand HIV neuropathogenesis. The main body of the thesis describes the outcomes of the RV254 Thai AHI cohort, in which all participants were enrolled during AHI and initiated ART within days after the diagnosis. Section 2 focuses on the findings during AHI, examining the determinant of HIV-1 RNA level in cerebrospinal fluid (CSF), the impact of concomitant syphilis, and the safety of performing lumbar punctures during AHI. Section 3 discusses the longitudinal outcomes of RV254 participants after ART, presenting their 6-year neurocognitive trajectory, the neuropsychological impact of switching from a Efavirenz-based ART to a Dolutegravir-based ART regimen, and the rare detection of HIV-1 RNA in CSF during plasma HIV-1 suppression (CSF HIV-1 escape). Section 4 explores the implications of CNS in HIV cure research. The findings suggest that HIV-1 invades the CNS during acute infection and causes abnormal neurological signs, neurocognitive dysfunction and depressive mood. Yet, prompt initiation of ART during AHI could reverse these abnormalities - RV254 participants on stable ART are generally free from neuropsychiatric complications frequently seen in other HIV-positive populations, highlighting the benefit of early ART in HIV infection

Predicting and analyzing HIV-1 adaptation to broadly neutralizing antibodies and the host immune system using machine learning

Thanks to its extraordinarily high mutation and replication rate, the human immunodeficiency virus type 1 (HIV-1) is able to rapidly adapt to the selection pressure imposed by the host immune system or antiretroviral drug exposure. With neither a cure nor a vaccine at hand, viral control is a major pillar in the combat of the HIV-1 pandemic. Without drug exposure, interindividual differences in viral control are partly influenced by host genetic factors like the human leukocyte antigen (HLA) system, and viral genetic factors like the predominant coreceptor usage of the virus. Thus, a close monitoring of the viral population within the patients and adjustments in the treatment regimens, as well as a continuous development of new drug components are indispensable measures to counteract the emergence of viral escape variants. To this end, a fast and accurate determination of the viral adaptation is essential for a successful treatment. This thesis is based upon four studies that aim to develop and apply statistical learning methods to (i) predict adaptation of the virus to broadly neutralizing antibodies (bNAbs), a promising new treatment option, (ii) advance antibody-mediated immunotherapy for clinical usage, and (iii) predict viral adaptation to the HLA system to further understand the switch in HIV-1 coreceptor usage. In total, this thesis comprises several statistical learning approaches to predict HIV-1 adaptation, thereby, enabling a better control of HIV-1 infections.Dank seiner außergewöhnlich hohen Mutations- und Replikationsrate ist das humane Immundefizienzvirus Typ 1 (HIV-1) in der Lage sich schnell an den vom Immunsystem des Wirtes oder durch die antiretrovirale Arzneimittelexposition ausgeübten Selektionsdruck anzupassen. Da weder ein Heilmittel noch ein Impfstoff verfügbar sind, ist die Viruskontrolle eine wichtige Säule im Kampf gegen die HIV-1-Pandemie. Ohne Arzneimittelexposition werden interindividuelle Unterschiede in der Viruskontrolle teilweise durch genetische Faktoren des Wirts wie das humane Leukozytenantigensystem (HLA) und virale genetische Faktoren wie die vorherrschende Korezeptornutzung des Virus beeinflusst. Eine genaue Überwachung der Viruspopulation innerhalb des Patienten, gegebenfalls Anpassungen der Behandlungsschemata sowie eine kontinuierliche Entwicklung neuer Wirkstoffkomponenten sind daher unerlässliche Maßnahmen, um dem Auftreten viraler Fluchtvarianten entgegenzuwirken. Für eine erfolgreiche Behandlung ist eine schnelle und genaue Bestimmung der Anpassung einer Variante essentiell. Die Thesis basiert auf vier Studien, deren Ziel es ist statistische Lernverfahren zu entwickeln und anzuwenden, um (1) die Anpassung von HIV-1 an breit neutralisierende Antikörper, eine neuartige vielversprechende Therapieoption, vorherzusagen, (2) den Einsatz von Antikörper-basierte Immuntherapien für den klinischen Einsatz voranzutreiben, und (3) die virale Anpassung von HIV-1 an das HLA-System vorherzusagen, um den Wechsel der HIV-1 Korezeptornutzung besser zu verstehen. Zusammenfassend umfasst diese Thesis mehrere statistische Lernverfahrenansätze, um HIV Anpassung vorherzusagen, wodurch eine bessere Kontrolle von HIV-1 Infektionen ermöglicht wird

Molecular characteristics of HIV-1 subtype C and its impact on therapeutic outcome in Ethiopia

HIV-1 is characterized by a high genetic diversity which poses several challenges and implications with regard to disease progression, drug resistance and outcome of antiretroviral therapy (ART). HIV-1 subtype C (HIV-1C) is the most rapidly expanding subtype accounting for half of the global disease and nearly all infections in Ethiopia, Southern Africa and India which are the regions with the highest burden of HIV-1 infection. Molecular characteristics of the virus in such epidemic success need to be explored to better understand this subtype. In the thesis, we analysed plasma samples and patient data collected during 2009-2011 in a large country-wide cohort, Advanced Clinical Monitoring of ART (ACM) which was established to evaluate the longitudinal effectiveness of ART as practiced in real life in Ethiopia. The overall aim was to investigate the molecular characteristics of HIV-1C and its impact on first line ART outcome in Ethiopia. Both genotypic and phenotypic molecular techniques were employed to characterize different regions of the viral genome. In papers I and II, population sequencing (PBSS) of the V3 loop of the HIV-1 envelope from therapy naïve, patients failing therapy, as well as HIV-1C sequences from Ethiopia dated 1984-2003 was used to assess the molecular epidemiology of HIV-1C in different geographic regions and the trend of viral tropism over the last decades. We also investigated the utility of different genotypic tropism prediction tools and the impact of the predicted viral co-receptor tropism on the outcome of standard first line ART. Our results showed that the Ethiopian epidemic is still monophylogenetic, exclusively dominated by HIV-1C, CCR5 tropic viruses. Furthermore, baseline tropism had an impact on outcome of standard first line ART. While each tool predicted tropism with comparable frequency, there was yet a large discordance between the tools. We elucidated this discordance further in paper III by employing an in-house phenotypic tropism method compared with the prediction by bioinformatics tools used in paper II as well as in vitro sensitivity of HIV-1CEth strains for the co-receptor antagonist maraviroc. The results showed underestimation of R5 co-receptor usage by bioinformatics tools and effectiveness of maraviroc in HIV-1C. Expanding the exploration further to pol gene, we employed PBSS and next generation sequencing (NGS) to assess the prevalence of surveillance drug resistance mutations (sDRM) to reverse transcriptase- and protease-inhibitors as well as occurrence of DRM by NGS to the novel category of integrase strand inhibitors. The results in paper IV showed that NGS detected sDRM associated with RT- and PI- inhibitors more often than PBSS and major INSTI DRMs were found in minor viral variants. Furthermore, DRM identified before treatment was associated with a poorer treatment outcome. In conclusion, viral tropism and drug resistance mutations at baseline have an impact on subsequent treatment outcome. Currently available genotypic tropism prediction tools need further improvement for use in HIV-1C. The Ethiopian epidemic remains uniquely dominated by R5 tropic HIV-1C since its introduction. Further investigations should be done to delineate associated molecular and epidemiological factors contributing to its uniqueness

Low-level HIV viremia during antiretroviral therapy

In most cases, antiretroviral therapy (ART) results in undetectable plasma HIV viral load (VL). Still, up to 25% of ART recipients may have detectable low-level viremia (LLV) of different amplitude and persistence. This thesis explores the impact of LLV during ART on virologic and clinical outcomes. Paper I–III are retrospective analyses based on InfCare HIV, a national quality register for people with HIV in Sweden. Time-updated viremia categories were used. Paper I included all participants in Malmö and Gothenburg between 1996 and 2016. Compared with viral suppression, individuals with LLV of 200–999 c/mL, but not 50–199 c/mL, had increased risk of future virologic failure (adjusted hazard ratio [aHR], 3.1; 95% confidence interval [CI], 1.4–7.0). LLV was associated with increased all-cause mortality, although this was not statistically significant in multivariable analysis. For paper II and III, we linked the nationwide InfCare HIV cohort (1996–2017) to national health registers. After 49 986 person-years of follow-up (median 5.7 years), 4177/6956 (60%) were classified as viral suppression, 339 (5%) as LLV of 50–199 c/mL, 258 (4%) as LLV of 200–999 c/mL, and 2182 (31%) as non-suppression. LLV of 50–999 c/mL was associated with increased all-cause mortality when compared with viral suppression (aHR, 2.2; 95% CI, 1.3–3.6). In subanalysis, LLV of 50–199 c/mL had an aHR of 2.2 (95% CI, 1.3–3.8) and LLV of 200–999 c/mL of 2.1 (95% CI, 0.96–4.7). LLV was not associated with AIDS, but individuals with LLV of 200–999 c/mL had increased risk of serious non-AIDS events (SNAE; cardiovascular disease being the most common diagnosis). Neither time-updated viremia category nor cumulative viremia during ART had statistically significant associations with cancer incidence. Higher pre-ART VL was associated with cancer (adjusted subhazard ratio, 1.4; 95% CI, 1.0–1.8). In subanalysis, the association between pre-ART VL and cancer was restricted to AIDS-defining malignancies and infection-related non–AIDS-defining cancer. In paper IV, we measured the levels of nine biomarkers in people with LLV (≥3 VLs in the range 50–999 c/mL) and matched controls with viral suppression. We found no difference in markers of inflammation and immune activation, but patients with LLV had higher levels of growth differentiation factor 15 (GDF-15) and D-dimer. Lastly, we analyzed 21 blood biomarkers and measures of cardiovascular function and structure in participants of a South African research cohort (paper V). We observed similar cardiovascular profiles among individuals with detectable viremia (50–999 c/mL in one measurement) and those with viral suppression (<50 c/mL). In conclusion, this thesis adds to mounting evidence that LLV is associated with inferior clinical outcomes in ART recipients. Specifically, we observed associations between LLV and virologic failure, all-cause mortality, and SNAE, respectively. Our findings suggest that this is likely not mediated through inflammation or immune activation, but elevated GDF-15 and D-dimer for people with LLV in repeated VL measurements could suggest higher cardiovascular risk. We found no evidence of increased risk of cancer or AIDS for people with LLV

Treatment strategies in HIV

The introduction of highly active antiretroviral therapy (HAART) has led to significant improvements in survival and morbidity for HIV-positive patients. Though HIV can now be well managed with treatment, interlinked barriers to successful treatment are still prevalent. In particular, low adherence to therapy, resistance to drugs and drug toxicity can have a considerable impact on the success of HAART. The potential of HAART is limited from the outset if patients are infected with a drug-resistant virus. Evidence suggests that a small minority of patients are starting HAART with drugs that the virus is resistant to, and consequently, are less likely to achieve virological suppression. A large proportion of resistance tests performed after patients‟ start HAART are not followed by a switch within 4 months of the result being received. This raises questions as to why the test was performed and whether limited future drug options are of concern. A single abnormal laboratory value may be the result of random fluctuations and may not necessarily be a reason for concern over drug toxicity. I derive a more stringent definition of an ALT flare and compare this definition with that commonly found in the literature. Treatment interruptions, perhaps due to drug toxicity, should not take place when the viral load is detectable. Patients who have achieved viral suppression after interrupting treatment and who have failed a higher number of HAART regimens are at a greater risk of viral rebound, though this risk is reduced substantially as duration of suppression increases. A score to characterise laboratory abnormalities is derived and used to predict mortality. Several methods were used; I felt the most appropriate was that based on the estimates from a regression model in which the current laboratory measurements were fitted; only three routinely measured laboratory measures were needed to calculate the score

Antiretroviral Drug Resistance Testing in Adult HIV-1 Infection: 2008 Recommendations of an International AIDS Society-USA Panel

Resistance to antiretroviral drugs remains an important limitation to successful human immunodeficiency virus type 1 (HIV-1) therapy. Resistance testing can improve treatment outcomes for infected individuals. The availability of new drugs from various classes, standardization of resistance assays, and the development of viral tropism tests necessitate new guidelines for resistance testing. The International AIDS Society-USA convened a panel of physicians and scientists with expertise in drug-resistant HIV-1, drug management, and patient care to review recently published data and presentations at scientific conferences and to provide updated recommendations. Whenever possible, resistance testing is recommended at the time of HIV infection diagnosis as part of the initial comprehensive patient assessment, as well as in all cases of virologic failure. Tropism testing is recommended whenever the use of chemokine receptor 5 antagonists is contemplated. As the roll out of antiretroviral therapy continues in developing countries, drug resistance monitoring for both subtype B and non-subtype B strains of HIV will become increasingly importan

HIV-1 viral load outcomes and the evolution of drug-resistance in low-income settings without virological monitoring

WHO guidelines recommend viral load monitoring for all HIV-1 positive patients on antiretroviral therapy (ART). However, few low-income countries have virological monitoring widely available, and patients may remain on virologically failing regimens. This could compromise future ART through the accumulation of drug resistance mutations and result in worse long-term clinical outcomes. The DART trial was conducted in Uganda and Zimbabwe and compared clinically driven monitoring with or without routine CD4 measurement in ART-naïve adult patients. Annual plasma viral load was retrospectively measured for 1,762 patients. This thesis investigates how no laboratory monitoring impacts virological failure and the development of drug resistance. Time to persistent virological failure was analysed, and analytical weights were calculated to correct for non-random sampling. The long-term durability of first-line ART was remarkable; 21% of patients on an NRTI-NNRTI regimen and 40% on a triple-NRTI regimen experienced persistent virological failure by 240 weeks. Routine CD4 monitoring did not reduce virological failure. Deaths after 48 weeks of ART are widely assumed to be due to virological failure or non-adherence. Analyses revealed that a surprisingly high number of these deaths (40%) occurred without virological criteria for treatment switch being met. Routine CD4 monitoring reduced the rate of death with virological failure but did not impact deaths with virological suppression. Cross-sectional analyses quantified HIV-1 drug resistance at the end of first-line ART. On NRTI-NNRTI regimens, 88% had NRTI resistance, and 66% had NNRTI resistance. Routine CD4 monitoring did not reduce the prevalence or extent of drug resistance. The order and rate of HIV-1 drug resistance mutations were explored using repeated genotypes within patients. On NRTI-NNRTI regimens, NRTI and NNRTI mutations developed at a rate of 0.96 and 0.21 per year respectively. Mutagenic tree models demonstrated that ART regimen influenced the order and rate in which mutations occurred

Predicting early and late first-line antiretroviral therapy virologic failure, and switch to second-line therapy in a military population in South Africa

The study involved retrospective data analysis using statistical methods to re-analyse data collected during a long-term study in a Human Immunodeficiency Virus infected population of South African National Defence Force employees and their dependents, where different parameters related to treatment and disease status of HIV infected patients were collected. This study attempted to identify possible predictors of both early and late occurrence of first-line antiretroviral therapy virologic failure, potential predictors of first-line antiretroviral virologic failure and for switching to second line therapy were identified.Dissertation (MSc)--University of Pretoria, 2018.HJF- Phidisa projectPharmacologyMScUnrestricte

An expert consensus for the management of chronic hepatitis B in Asian Americans.

BACKGROUND: Hepatitis B virus (HBV) infection is common with major clinical consequences. In Asian Americans, the HBsAg carrier rate ranges from 2% to 16% which approximates the rates from their countries of origin. Similarly, HBV is the most important cause of cirrhosis, hepatocellular carcinoma (HCC) and liver related deaths in HBsAg positive Asians worldwide. AIM: To generate recommendations for the management of Asian Americans infected with HBV. METHODS: These guidelines are based on relevant data derived from medical reports on HBV from Asian countries as well as from studies in the HBsAg positive Asian Americans. The guidelines herein differ from other recommendations in the treatment of both HBeAg positive and negative chronic hepatitis B (CHB), in the approach to HCC surveillance, and in the management of HBV in pregnant women. RESULTS: Asian American patients, HBeAg positive or negative, with HBV DNA levels \u3e2000 IU/mL (\u3e10 CONCLUSIONS: Application of the recommendations made based on a review of the relevant literature and the opinion of a panel of Asian American physicians with expertise in HBV treatment will inform physicians and improve patient outcomes