Academic literature on the topic 'Immunoloigcal and Virological Dynamics'

HIV cure studies require patients to enter an analytical treatment interruption (ATI). Here, we describe previously unanalyzed data that sheds light on ATI dynamics in PLHIV (People Living with HIV). We present drug resistance mutation dynamics on the pol gene among individuals with antiretroviral virological failure who underwent ATI. The study involved a 12-week interruption in antiretroviral therapy (ART), monitoring of viral load, CD4+/CD8+ T cell counts, and sequencing of the pol gene from 38 individuals experiencing virological failure and harboring 3-class resistant HIV strains: nucleoside reverse transcriptase inhibitors (NRTI) non-nucleoside inhibitors (NNRTI), and protease inhibitors (PI). Protease and reverse transcriptase regions of the pol gene were sequenced at baseline before ATI and every four weeks thereafter from PBMCs and at baseline and after 12 weeks from plasma HIV RNA using population-based Sanger sequencing. Average viral load increased 0.559 log10 copies per milliliter. CD4+ T cell count decreased as soon as ART was withdrawn, an average loss of 99.0 cells/mL. Forty-three percent of the mutations associated with antiretroviral resistance in PBMCs disappeared and fifty-seven percent of the mutations in plasma reverted to wild type, which was less than the 100% reversion expected. In PBMC, the PI mutations reverted more slowly than reverse transcriptase mutations. The patients were projected to need an average of 33.7 weeks for PI to revert compared with 20.9 weeks for NRTI and 19.8 weeks for NNRTI. Mutations in the pol gene can cause virological failure and difficulty in re-establishing effective virological suppression.

The aim of this work is to present a virological model for cancer therapy that includes the innate immune response and saturation effect. The presented model combines both the evolution of a logistic growing tumor and time delay which stands for the period of the viral lytic cycle. We use the delay differential equation in order to model this time which also means the time needed for the infected tumor cells to produce new virions after viral entry. We show that the delayed model has four equilibria which are the desired outcome therapy equilibrium, the complete failure therapy equilibrium, the partial success therapy free-immune equilibrium when the innate immune response has not been established, and the partial success therapy equilibrium with immune response. Furthermore, the stability analysis of equilibria and the Hopf bifurcation are properly exhibited.

Background Early identification of non-responders to interferon-α and development of stopping rules are needed in patients with chronic hepatitis B to reduce treatment-related costs and morbidity. Methods In total, 47 patients with hepatitis B e antigen (HBeAg)-positive chronic hepatitis B received pegylated interferon-α2b for 8 weeks, lamivudine plus pegylated interferon-α2b combination therapy for 24 weeks and lamivudine monotherapy for 28 weeks. Sustained virological response was defined as HBeAg seroconversion and hepatitis B virus (HBV) DNA<105 copies/ml at the end of treatment and after 52 weeks of follow-up. The early HBV DNA data from the first 12 weeks of therapy were fitted by a viral kinetic model. Results Cutoff values for prediction of sustained virological response were defined as a rate of infected cell loss δ≥0.005 per day (negative predictive value [NPV] 100% and positive predictive value [PPV] 33.3%) and log values of the area under the mathematically predicted HBV DNA curve between baseline and week 12 of therapy ≤8.9 log10 copies/ml x days (NPV 100% and PPV 50%). By the latter cutoff, 25/36 (69.4%) patients without sustained virological response could be identified after 12 weeks of therapy. Conclusions In the present study, mathematical modelling of viral dynamics allowed prediction of sustained virological response after 12 weeks of therapy. Virodynamic predictors for sustained virological response should be further validated. The area under the mathematically predicted HBV DNA curve seems a promising candidate for potential cutoff values as it summarizes the influence of baseline HBV DNA and treatment effects.

Intensified surveillance during the 2009 A/H1N1 influenza pandemic in Israel resulted in large virological and serological datasets, presenting a unique opportunity for investigating the pandemic dynamics. We employ a conditional likelihood approach for fitting a disease transmission model to virological and serological data, conditional on clinical data. The model is used to reconstruct the temporal pattern of the pandemic in Israel in five age-groups and evaluate the factors that shaped it. We estimate the reproductive number at the beginning of the pandemic to be R = 1.4. We find that the combined effect of varying absolute humidity conditions and school vacations (SVs) is responsible for the infection pattern, characterized by three epidemic waves. Overall attack rate is estimated at 32% (28–35%) with a large variation among the age-groups: the highest attack rates within school children and the lowest within the elderly. This pattern of infection is explained by a combination of the age-group contact structure and increasing immunity with age. We assess that SVs increased the overall attack rates by prolonging the pandemic into the winter. Vaccinating school children would have been the optimal strategy for minimizing infection rates in all age-groups.

The aim of the study was to evaluate the effectiveness of triple antiretroviral theтру, including domestic product Phosphazide in 18 HIV-infected patients during 48 weeks. There was determined the dynamics of the clinical manifestations of the disease, the parameters of viral load and CD4 lymphocytes before antiretroviral therapy (ART), and 4, 12, 24, 36 and 48 weeks after its use. The study showed high virological and sufficient immunologic efficacy of this schedule.

ABSTRACT Lamivudine was the first approved inhibitor of hepatitis B virus (HBV) reverse transcriptase (RT). Lamivudine resistance develops in 53% to 76% of patients after 3 years of treatment. We extensively characterized the dynamics of HBV quasispecies variant populations in four HBV-infected patients who developed lamivudine resistance. Virological breakthrough was preceded by 2 to 4 months by the emergence of quasispecies variants bearing amino acid substitutions at RT position 204, i.e., within the YMDD catalytic motif (rtM204V/I). Three patients had a gradual switch from a YMDD variant population at baseline to a 100% lamivudine-resistant variant population, whereas the remaining patient had a fluctuating pattern of resistance variant dynamics. Careful analysis of amino acid substitutions located outside domain C of HBV RT, including those known to partially restore replication capacities in vitro, showed that the in vivo replication of HBV variants is driven by multiple forces, including intrinsic replicative advantages conferred by mutations accumulating outside domain C and the changing environment in which these variants replicate. Our findings also suggest that individual treatment optimization will require sensitive methods capable of detecting the emergence of viral resistance before the relevant variants acquire optimal replicative capacities.

A river intensively used along its entire course for extracting potable water and for discharging domestic and industrial effluents permanently carries a high load of viruses, including hepatitis A and rotaviruses. In the areas supplied with potable water from this river hepatitis A is endemic. The river has been investigated four times at 16 or more sampling points throughout its course in the years 1981, 1982 and 1983. Coincident with the virological investigation, biological, microbiological and chemical examinations were conducted with the same water sample. At some representatively distributed sampling points along the river course, tests for heavy metals (Cd, Ni, Cu, Cr, Pb) and selected chemical compounds were also performed. The virological quality of the river water largely depends on the virus input via domestic sewage. Statistically significant correlations have been found between virus level, pH, NH4+ and NO3−. Amoebae species are likely to counteract viruses. Knowing the dynamics of river water exploitation above the extraction sites, a model for the estimation of virus content in the raw water could be developed.

ABSTRACT Despite the extensive quantitative and qualitative knowledge about therapeutic regimens and the molecular biology of HIV/AIDS, the eradication of HIV infection cannot be achieved with available antiretroviral regimens. HIV drug resistance remains the most challenging factor in the application of approved antiretroviral agents. Previous investigations and existing HIV/AIDS models and algorithms have not enabled the development of long-lasting and preventive drug agents. Therefore, the analysis of the dynamics of drug resistance and the development of sophisticated HIV/AIDS analytical algorithms and models are critical for the development of new, potent antiviral agents, and for the greater understanding of the evolutionary behaviours of HIV. This study presents novel computational methods for the analysis of drug-resistance dynamics, including: viral sequences, phenotypic resistance, immunological and virological responses and key clinical data, from HIV-infected patients at Royal Prince Alfred Hospital in Sydney. The lability of immunological and virological responses is analysed in the context of the evolution of antiretroviral drug-resistance mutations. A novel Bayesian algorithm is developed for the detection and classification of neutral and adaptive mutational patterns associated with HIV drug resistance. To simplify and provide insights into the multifactorial interactions between viral populations, immune-system cells, drug resistance and treatment parameters, a Bayesian graphical model of drug-resistance dynamics is developed; the model supports the exploration of the interdependent associations among these dynamics.

Doctor of Philosophy(PhD)
ABSTRACT Despite the extensive quantitative and qualitative knowledge about therapeutic regimens and the molecular biology of HIV/AIDS, the eradication of HIV infection cannot be achieved with available antiretroviral regimens. HIV drug resistance remains the most challenging factor in the application of approved antiretroviral agents. Previous investigations and existing HIV/AIDS models and algorithms have not enabled the development of long-lasting and preventive drug agents. Therefore, the analysis of the dynamics of drug resistance and the development of sophisticated HIV/AIDS analytical algorithms and models are critical for the development of new, potent antiviral agents, and for the greater understanding of the evolutionary behaviours of HIV. This study presents novel computational methods for the analysis of drug-resistance dynamics, including: viral sequences, phenotypic resistance, immunological and virological responses and key clinical data, from HIV-infected patients at Royal Prince Alfred Hospital in Sydney. The lability of immunological and virological responses is analysed in the context of the evolution of antiretroviral drug-resistance mutations. A novel Bayesian algorithm is developed for the detection and classification of neutral and adaptive mutational patterns associated with HIV drug resistance. To simplify and provide insights into the multifactorial interactions between viral populations, immune-system cells, drug resistance and treatment parameters, a Bayesian graphical model of drug-resistance dynamics is developed; the model supports the exploration of the interdependent associations among these dynamics.

L'infection par le Virus de l'Immunodéficience Simienne (SIV) persiste dans l'organisme en raison des cellules infectées contenant le génome viral intégré. Ces cellules dites « Réservoirs » constituent l'obstacle majeur à l'éradication virale et sont au cœur de nouveaux challenges thérapeutiques. Le modèle simien permet d'explorer les tissus réservoirs et l'évolution virale dans l'organisme. Dans une première partie, l'objectif de notre travail a été de caractériser la dynamique du SIV dans le sang et les tissus, en l'absence de traitement. Dans le cadre du programme P-Visconti, 6 macaques ont été infectés par du SIVmac et ont été suivis pendant 6 mois. Nous avons mis au point des techniques ultrasensibles de quantification d'ADN SIV (niveau d'infection) et d'ARN SIV associés aux cellules (caARN SIV) exprimant la capacité transcriptionnelle des cellules infectées. Nous avons développé une méthode de séquençage à haut débit et des outils de bio-informatique pour une analyse en profondeur de plus de 60 millions de séquences, permettant de décrire l'évolution et le nombre de variants viraux dans le sang et les tissus. Nous montrons que les cinétiques du nombre de cellules sanguines infectées et leur niveau transcriptionnel reflétaient la cinétique de virémie plasmatique. De plus, l'évolution de la diversité génétique (nombre de variants et distance génétique) mimait l'évolution des 2 marqueurs. Les variants présents dans l'inoculum tendaient à disparaître dès J28 dans le plasma mais persistaient dans les cellules sanguines. La proportion des variants majoritaires évoluait au cours du temps et, malgré un inoculum identique, une grande hétérogénéité de niveaux d'infection et de diversité génétique a pu être observée entre les singes. À 6 mois d'infection, de nombreux tissus ont été collectés à l'euthanasie. Nous montrons une infection disséminée et réplicative dans 26 sites anatomiques, y compris dans la peau et le tissu adipeux. Les tissus lymphoïdes secondaires présentaient les niveaux d'infection et d'activité transcriptionnelle les plus élevés, lesquels étaient associés à des profils de quasi-espèces virales les plus éloignées de l'inoculum, soulignant le rôle majeur de l'activité ganglionnaire à l'origine de l'évolution virale. Le niveau d'infection de nombreux tissus était corrélé à celui du sang périphérique au moment du pic de réplication. Les différents tissus lymphoïdes et plusieurs tissus non lymphoïdes présentaient des variants majoritaires communs, témoignant d'une très importante circulation de virions et/ou de cellules infectées entre les tissus (Manuscrit 1). Dans une deuxième partie, nous avons étudié un modèle de singes infectés par du SIV, et 12 animaux sur 16 ont montré un contrôle viral spontané (Singes «contrôleurs», SIC). Aucune différence n'a été observée au niveau sanguin, au pic (J15) entre les SIC et les singes non-contrôleurs. En revanche, les SIC avaient un niveau d'infection significativement plus faible dans les ganglions dès J15. De même, après 18 mois, les charges ADN SIV apparaissaient plus faibles dans tous les tissus des SIC. Parallèlement, sur le plan immunologique (C. Pereira et al., I. Pasteur), l'activité suppressive des cellules T CD8 spécifiques du SIV s'est développée au cours du temps et était liée à des niveaux de réservoir viral plus faibles (Manuscrit 2). La modélisation mathématique combinant les résultats immuno-virologiques (V. Madelain et al., Paris 7) a montré une décroissance biphasique de l'ADN SIV après le pic de virémie chez les SIC, liée à 2 populations cellulaires (1 à demi-vie courte et 1 à demi-vie longue). Ces résultats indiquent les cellules à cibler dans le contexte des études de rémission et/ou cure (Manuscrit 3). L'ensemble de ces données démontre le rôle clé des tissus lymphoïdes dans la dynamique de l'infection et dans la diffusion des variants viraux. La forte dispersion virale souligne la nécessité d'utiliser des molécules diffusant dans tout l'organisme
Simian Immunodeficiency Virus (SIV) infection persists in the body with infected cells containing the integrated viral genome. These cells called "reservoirs" constitute the major barrier to viral eradication and are focus of interest of new therapeutic challenges. The simian model enables the exploration of tissue reservoirs and viral evolution throughout the whole body. In a first part, the aim of our work was to characterize the dynamics of SIV in the blood and tissues in the absence of treatment. In the P-Visconti program, six macaques were infected by SIVmac251 and were followed 6 months before euthanasia. We developed ultrasensitive assays for the SIV DNA quantification (cell infection level) and cell-associated SIV RNA (caSIV RNA), expressing the transcriptional ability of infected cells. In addition, we developed a high throughput sequencing method and bioinformatics tools for in-depth analysis of more than 60 million reads, describing the evolution and number of viral variants in blood and tissues. We showed that the kinetics of the number of infected blood cells and their transcriptional level reflected the kinetics of plasma viremia. Moreover, the evolution of genetic diversity (number of variants and genetic distance) mimicked the evolution of the two markers. The variants constituting the inoculum tended to disappear as soon as day (D)28 in the plasma but persisted longer in the blood cells. The proportion of major variants evolved over time and, despite identical inoculum, a great heterogeneity of infection levels and genetic diversity could be observed among the monkeys. At 6 months post infection, many tissues were collected at euthanasia. We showed a disseminated and replicative infection over 26 anatomical sites, including skin and adipose tissues. Secondary lymphoid organs exhibited the highest levels of infection and transcriptional activity, which were associated with the most divergent viral quasi-species profiles from the inoculum, highlighting the major role of lymph nodes in the viral evolution. Infection level of many tissues was correlated with that observed in blood at the peak of replication. The different lymphoid tissues and several non-lymphoid tissues shared some major variants, indicating high exchanges of virions and/or infected cells between tissues (Manuscript 1). In a second part, we examined a model of SIVmac infected macaques, and 12 out of 16 animals exhibited spontaneous viral control (Simian "controllers": SIC). No difference of viral level was observed in blood at the peak (D15) between SIC and non-controller macaques. In contrast, SIC had a significantly lower level of infection in the lymph nodes since D15. Moreover, after 18 months, SIV DNA loads appeared lower in all SIC tissues. In addition, immunological studies (C. Pereira et al., I. Pasteur) showed that suppressive activity of SIV-specific CD8+ T cells has been developed over time and was related to lower viral reservoir levels (Manuscript 2). Mathematical modeling combining these immuno-virological data (V. Madelain et al., Univ Paris 7) showed a biphasic decay of SIV DNA after the peak of viremia in SIC, that could be related to 2 cell populations (one with short half-life and the other with a long half-life). These results indicate which cells have to been targeted in the context of remission and/or cure studies (Manuscript 3). All of these data demonstrate the key role of lymphoid tissues in the infection dynamics and in viral variants diffusion and diversification. The strong viral spread highlights the need to use molecules that penetrate throughout the whole body

Background: Multiple factors contribute to mother-to-child transmission (MTCT) of HIV-1, including virological, obstetric and biological factors. Other possible contributory determinants for high MTCT rates include immunological factors such as host genetics and viral genetic variations. Despite several therapeutic, prophylactic and obstetric interventions to reduce the proportion of infants infected during labour and delivery, mechanisms for intrapartum HIV-1 transmission remain elusive and current interventions, could, therefore remain sub-optimal. Much controversy has surrounded the correlation of HIV-1 RNA (viral load) in the systemic and genital compartments of women. The influence of short-term antiretroviral (ARV) drugs on genital tract HIV-1 is also unclear. At the time the present study was initiated, a regimen of maternal intrapartum and neonatal postpartum single-dose Nevirapine (sdNVP) was the standard of care for the prevention of mother-to-child transmission (PMTCT). In most low and middle-income countries, including South Africa, sdNVP has been documented as effective intrapartum HIV-1 prevention based on plasma pharmacokinetic levels, decreased viral loads (HIV-1 RNA) and reduced rates of intrapartum transmission, yet operational studies continue to report high intrapartum transmission rates despite the administration of sdNVP. As a result perinatal HIV-1 transmission remains a significant public health concern in several African countries. Aim: The primary aim of this study was to describe the pharmacological dynamics of Nevirapine in association with virological and immunological risk factors for intrapartum HIV-1 transmission in a South African PMTCT programme where sdNVP was the standard of care. Methods: Following regulatory approval from the Biomedical Research Ethics Committee at the University of KwaZulu-Natal (UKZN), one hundred and twenty pregnant HIV-infected women who received the sdNVP regimen for prevention of mother-to-child HIV-1 transmission were enrolled between April-December 2006 at King Edward VIII Hospital (KEH) in Durban. Blood and cervicovaginal lavage (CVL) samples were collected from women at pre-NVP (during pregnancy) and post-NVP dosing (during labour/delivery). In addition to infant blood sampling at birth (post-NVP), postnatal infants were assessed at four and six weeks postnatally. Pharmacological laboratory investigations involved measurement of NVP drug concentration by Tandem Mass spectrophotometry. Virological investigations comprised HIV-1 RNA (viral load) quantitation, HIV-1 drug resistance testing (HIV-1 transmitting women only) and HIV-1 DNA PCR testing (infants only). Immunological investigations were only undertaken in a selected case-control subset of HIV-1 transmitting women and their infants. In this component, laboratory investigations included the determination of CCL3 and CCL3-L1 gene copy numbers, identification of single nucleotide polymorphisms (SNP’s) and haplotype characterisation of the CCL3 gene. All women were also screened for the presence of sexually transmitted infections (STI’s) during pregnancy. Results: One hundred and twenty women were enrolled onto this study. Of these, 110 women delivered 117 live infants (103 singletons and 7 twin pairs). Twelve (10.9%) women transmitted HIV-1 to their infants, while 95 (86.0%) were classified as non-transmitters. As a result of seven twin deliveries, the infant cohort comprised of 117 infants in total. Following two separate DNA PCR tests, HIV-1 infection was identified in 14 (11.9%) of study infants while the remaining 90 (76.9%) were exposed-uninfected. HIV infection status remained unknown for 13 infants due to infant demise (1.7%), lost to follow-up (7.7%) or study withdrawal (1.7%). During active labour (sampling that was best representative of the intrapartum phase) and within 20 hours of dosing, the median NVP concentration of 1070 ng/ml in the maternal systemic compartment was almost 44 times higher than the NVP levels detected in the genital compartment [24.5 ng/ml] (p < 0.001). NVP drug levels were below the 100 ng/ml therapeutic target in seven (13.7%) of 51 plasma and in all 39 CVL samples. While no significant association was found between NVP concentration in the systemic compartment and HIV-1 transmission (p = 0.4), this association was statistically significant in the genital compartment(p = 0.02). The median plasma NVP level detected among infants at birth was 83 times above the IC50 WT (10 ng/ml) and eight times higher than the 100 ng/ml therapeutic target for NVP. More than 71.0% of the infants achieved NVP drug levels above the therapeutic target. In general, higher levels of HIV-1 RNA (viral load) were observed in maternal plasma when compared to CVL. Following intrapartum sdNVP dosing, reduction in HIV-1 RNA levels did occur, however R80.0% of the women experienced no change to their HIV-1 RNA levels in both systemic and genital compartments during active labour. These findings were further supported by the strong correlation observed when comparing pre and post-NVP HIV-1 RNA levels in both maternal systemic [r = 0.81, p < 0.0001] and genital compartments [r = 0.80, p < 0.0001] during active labour. HIV-1 transmitting women had significantly higher viral loads than their non-transmitting counterparts in systemic and genital compartments, before and after intrapartum sdNVP administration. In terms of perinatal transmission this observation was only statistically significant for plasma (p = 0.02) and not CVL (p = 0.7). Maternal viral load was inversely correlated with maternal CD4 cell counts in both systemic and genital compartments. Almost 40.0% of women in this study had at least one type of STI detected during pregnancy. Maternal STI’s were detected in four (66.6%) intrapartum transmitting women and in 38 (38.8%) of non-transmitting women. No significant association was observed between the presence of maternal STI’s and the risk for intrapartum MTCT (p = 0.2,RR: 2.90, 95% CI: 0.60-15.40). The presence of maternal STI’s was associated with higher median viral loads in both systemic and genital compartments of all women, independent of intrapartum HIV-1 transmission. Despite trial-like conditions and optimal sdNVP dosing, the overall MTCT rate in this exclusively formula-fed cohort was 11.9%, of which 50.0% were in utero and 50.0% were intrapartum HIV-1 transmissions. In utero and intrapartum MTCT rates were 5.9% and 5.9% respectively. Discussion/Conclusion: Detectable CVL HIV-1 RNA that correlated well with plasma HIV-1 RNA, in conjunction with sub-optimal NVP drug concentration in maternal CVL during active labour, suggests that intrapartum HIV-1 infected women continue to act as reservoirs for both vertical and horizontal HIV-1 transmission throughout the duration of pregnancy. These findings confirm that the role of sdNVP in PMTCT was primarily one of infant prophylaxis. This was further supported by relatively unchanged maternal HIV-1 RNA (viral load) during active labour, in both systemic and genital compartments. Early identification of women who need highly active antiretroviral therapy (HAART), and initiation of such therapy as early as possible during pregnancy, not only benefits maternal health but remains the best prophylaxis against mother-to-child HIV-1 transmission. Universal access to HAART and improving strategies to optimize coverage of the current dual ARV regimen sdNVP and Zidovudine for PMTCT remain urgent research priorities in several resource-limited settings. Ongoing STI counseling, intensive screening/testing of women and their partners together promotion of condom usage, safer sex practices and aggressive STI treatment are simple interventions with tremendous impact for PMTCT in resource-limited settings.
Thesis (Ph.D.)-University of KwaZulu-Natal, Durban, 2009.