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HIV viral dynamics

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https://www.readbyqxmd.com/read/27921997/comparative-molecular-dynamics-study-of-dimeric-and-monomeric-forms-of-hiv-1-protease-in-ligand-bound-and-unbound-state
#1
Monikaben Padariya, Umesh Kalathiya
Human immunodeficiency virus type 1 protease is a viral-encoded enzyme and it is essential for replication and assembly of the virus. Inactivation of HIV-1 protease causes production of immature, noninfectious viral particles and thus HIV-1 protease is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different ligands (COM5 - designed in our previous study, and Darunavir) and made effort to understand dynamics behaviour of our designed compound COM5...
December 6, 2016: General Physiology and Biophysics
https://www.readbyqxmd.com/read/27920778/the-dynamics-of-t-and-b-cells-in-lymph-node-during-chronic-hiv-infection-tfh-and-hiv-unhappy-dance-partners
#2
REVIEW
Jung Joo Hong, Kyu-Tae Chang, Francois Villinger
Although the dynamics of germinal center (GC) formation, follicular helper T (TFH) cell recruitment to B cell follicles within lymphoid organs, and changes of lymphoid tissue architecture in HIV/SIV infection have been documented, the underlying immunopathology remains unclear. Here, we summarize what is known regarding the kinetics of TFH cells and GC B cells during the course of infection as well as the potential immunopathological features associated with structural changes in the lymphoid compartment. This review also explores the implications of cell dynamics in the formation and maintenance of viral reservoirs in hyperplastic follicles of secondary lymphoid organs before and after viral suppressive antiretroviral therapy...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27914874/transmission-networks-and-risk-of-hiv-infection-in-kwazulu-natal-south-africa-a-community-wide-phylogenetic-study
#3
Tulio de Oliveira, Ayesha B M Kharsany, Tiago Gräf, Cherie Cawood, David Khanyile, Anneke Grobler, Adrian Puren, Savathree Madurai, Cheryl Baxter, Quarraisha Abdool Karim, Salim S Abdool Karim
BACKGROUND: The incidence of HIV infection in young women in Africa is very high. We did a large-scale community-wide phylogenetic study to examine the underlying HIV transmission dynamics and the source and consequences of high rates of HIV infection in young women in South Africa. METHODS: We did a cross-sectional household survey of randomly selected individuals aged 15-49 years in two neighbouring subdistricts (one urban and one rural) with a high burden of HIV infection in KwaZulu-Natal, South Africa...
November 30, 2016: Lancet HIV
https://www.readbyqxmd.com/read/27907076/clinical-determinants-of-hiv-1b-between-host-evolution-and-their-association-with-drug-resistance-in-pediatric-patients
#4
Israel Pagán, Patricia Rojas, José Tomás Ramos, África Holguín
Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution...
2016: PloS One
https://www.readbyqxmd.com/read/27906057/the-hiv-treatment-cascade-and-care-continuum-updates-goals-and-recommendations-for-the-future
#5
REVIEW
Emma Sophia Kay, D Scott Batey, Michael J Mugavero
The HIV care continuum is a framework that models the dynamic stages of HIV care. The continuum consists of five main steps, which, at the population level, are depicted cross-sectionally as the HIV treatment cascade. These steps include diagnosis, linkage to care (LTC), retention in care (RiC), adherence to antiretroviral therapy (ART), and viral suppression. Although the HIV treatment cascade is represented as a linear, unidirectional framework, persons living with HIV (PLWH) often experience the care continuum in a less streamlined fashion, skip steps altogether, or even exit the continuum for a period of time and regress to an earlier stage...
November 8, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27903772/diverse-activities-of-viral-cis-acting-rna-regulatory-elements-revealed-using-multi-color-long-term-single-cell-imaging
#6
Ginger M Pocock, Laraine L Zimdars, Ming Yuan, Kevin W Eliceiri, Paul Ahlquist, Nathan M Sherer
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other post-transcriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multi-color, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus) and an intron-retaining transcript encoded by the cellular NXF1 gene...
November 30, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27893864/cost-effectiveness-of-the-one4all-hiv-linkage-intervention-in-guangxi-zhuang-autonomous-region-china
#7
Xiao Zang, Houlin Tang, Jeong Eun Min, Diane Gu, Julio S G Montaner, Zunyou Wu, Bohdan Nosyk
BACKGROUND: In Guangxi Zhuang Autonomous Region, China, an estimated 80% of newly-identified antiretroviral therapy (ART)-eligible patients are not engaged in ART. Delayed ART uptake ultimately translates into high rates of HIV morbidity, mortality, and transmission. To enhance HIV testing receipt and subsequent treatment uptake in Guangxi, the Chinese Center for Disease Control and Prevention (CDC) executed a cluster-randomized trial to assess the effectiveness and cost-effectiveness of a streamlined HIV testing algorithm (the One4All intervention) in 12 county-level hospitals...
2016: PloS One
https://www.readbyqxmd.com/read/27888126/understanding-the-complex-evolution-of-rapidly-mutating-viruses-with-deep-sequencing-beyond-the-analysis-of-viral-diversity
#8
REVIEW
Preston Leung, Auda A Eltahla, Andrew R Lloyd, Rowena A Bull, Fabio Luciani
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts...
November 22, 2016: Virus Research
https://www.readbyqxmd.com/read/27858869/switch-of-predicted-hiv-1-tropism-in-treated-subjects-and-its-association-with-disease-progression
#9
Antonella Castagna, Laura Monno, Stefania Carta, Laura Galli, Stefania Carrara, Valentina Fedele, Grazia Punzi, Iuri Fanti, Pietro Caramello, Alessandro Cozzi Lepri, Andrea De Luca, Francesca Ceccherini-Silberstein, Antonella d'Arminio Monforte
Dynamics of human immunodeficiency virus type 1 (HIV-1) tropism after antiretroviral therapy (ART) initiation and their association with disease progression are poorly investigated.This was a cohort study on subjects from the ICONA cohort receiving ART with persistently detectable (PD) or persistently undetectable (PU) viral load (VL) and with stored plasma or peripheral blood mononuclear cell (PBMC) samples at 2 time-points (T1, T2) after ART initiation. HIV-1 co-receptor tropism was determined by V3-loop sequencing and the geno2pheno algorithm...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27831948/hiv-surveillance-combining-an-assay-for-identification-of-very-recent-infection-and-phylogenetic-analyses-on-dried-spots
#10
Denys Brand, Jean Capsec, Antoine Chaillon, Françoise Cazein, Stéphane Le Vu, Alain Moreau, Josiane Pillonel, Sylvie Brunet, Damien Thierry, Leslie Guillon-Grammatico, Florence Lot, Francis Barin
BACKGROUND: Transmitted/founder (T/F) viruses isolated at the early stage of infection are indicators of the variants that are spreading within a population. The French reporting system for new HIV diagnoses is linked to a virological surveillance using dried serum spots (DSS). METHODS: We combined an immunoassay for very recent infection (VRI < 31 days) to a phylogenetic analysis of T/F viruses and sociodemographic information to analyze the dynamics of the HIV-1 epidemic during a 3-year period...
November 7, 2016: AIDS
https://www.readbyqxmd.com/read/27830755/dynamic-oligomerization-of-integrase-orchestrates-hiv-nuclear-entry
#11
Doortje Borrenberghs, Lieve Dirix, Flore De Wit, Susana Rocha, Jolien Blokken, Stéphanie De Houwer, Rik Gijsbers, Frauke Christ, Johan Hofkens, Jelle Hendrix, Zeger Debyser
Nuclear entry is a selective, dynamic process granting the HIV-1 pre-integration complex (PIC) access to the chromatin. Classical analysis of nuclear entry of heterogeneous viral particles only yields averaged information. We now have employed single-virus fluorescence methods to follow the fate of single viral pre-integration complexes (PICs) during infection by visualizing HIV-1 integrase (IN). Nuclear entry is associated with a reduction in the number of IN molecules in the complexes while the interaction with LEDGF/p75 enhances IN oligomerization in the nucleus...
November 10, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27826353/the-hiv-treatment-cascade-and-care-continuum-updates-goals-and-recommendations-for-the-future
#12
REVIEW
Emma Sophia Kay, D Scott Batey, Michael J Mugavero
The HIV care continuum is a framework that models the dynamic stages of HIV care. The continuum consists of five main steps, which, at the population level, are depicted cross-sectionally as the HIV treatment cascade. These steps include diagnosis, linkage to care (LTC), retention in care (RiC), adherence to antiretroviral therapy (ART), and viral suppression. Although the HIV treatment cascade is represented as a linear, unidirectional framework, persons living with HIV (PLWH) often experience the care continuum in a less streamlined fashion, skip steps altogether, or even exit the continuum for a period of time and regress to an earlier stage...
2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27824626/reducing-hiv-infection-in-people-who-inject-drugs-is-impossible-without-targeting-recently-infected-subjects
#13
Tetyana I Vasylyeva, Samuel R Friedman, Jose Lourenco, Sunetra Gupta, Angelos Hatzakis, Oliver G Pybus, Aris Katzourakis, Pavlo Smyrnov, Timokratis Karamitros, Dimitrios Paraskevis, Gkikas Magiorkinis
OBJECTIVE: Although our understanding of viral transmission among people who inject drugs (PWID) has improved, we still know little about when and how many times each injector transmits HIV throughout the duration of infection. We describe HIV dynamics in PWID to evaluate which preventive strategies can be efficient. DESIGN: Due to the notably scarce interventions, HIV-1 spread explosively in Russia and Ukraine in 1990s. By studying this epidemic between 1995 and 2005, we characterized naturally occurring transmission dynamics of HIV among PWID...
November 28, 2016: AIDS
https://www.readbyqxmd.com/read/27821283/dynamic-conformational-changes-in-the-rhesus-trim5%C3%AE-dimer-dictate-the-potency-of-hiv-1-restriction
#14
Rajan Lamichhane, Santanu Mukherjee, Nikolai Smolin, Raymond F Pauszek, Margret Bradley, Jaya Sastri, Seth L Robia, David Millar, Edward M Campbell
The TRIM5α protein from rhesus macaques (rhTRIM5α) mediates a potent inhibition of HIV-1 infection via a mechanism that involves the abortive disassembly of the viral core. We have demonstrated that alpha-helical elements within the Linker 2 (L2) region, which lies between the SPRY domain and the Coiled-Coil domain, influence the potency of restriction. Here, we utilize single-molecule FRET analysis to reveal that the L2 region of the TRIM5α dimer undergoes dynamic conformational changes, which results in the displacement of L2 regions by 25 angstroms relative to each other...
November 4, 2016: Virology
https://www.readbyqxmd.com/read/27819062/reconstitution-of-peripheral-t-cells-by-tissue-derived-ccr4-central-memory-cells-following-hiv-1-antiretroviral-therapy
#15
Yolanda D Mahnke, Kipper Fletez-Brant, Irini Sereti, Mario Roederer
BACKGROUND: Highly active antiretroviral therapy induces clinical benefits to HIV-1 infected individuals, which can be striking in those with progressive disease. Improved survival and decreased incidence of opportunistic infections go hand in hand with a suppression of the plasma viral load, an increase in peripheral CD4(+) T-cell counts, as well as a reduction in the activation status of both CD4(+) and CD8(+) T cells. METHODS: We investigated T-cell dynamics during ART by polychromatic flow cytometry in total as well as in HIV-1-specific CD4(+) and CD8(+) T cells in patients with advanced disease...
2016: Pathogens & Immunity
https://www.readbyqxmd.com/read/27799557/cryo-em-structure-of-a-cd4-bound-open-hiv-1-envelope-trimer-reveals-structural-rearrangements-of-the-gp120-v1v2-loop
#16
Haoqing Wang, Alexander A Cohen, Rachel P Galimidi, Harry B Gristick, Grant J Jensen, Pamela J Bjorkman
The HIV-1 envelope (Env) glycoprotein, a trimer of gp120-gp41 heterodimers, relies on conformational flexibility to function in fusing the viral and host membranes. Fusion is achieved after gp120 binds to CD4, the HIV-1 receptor, and a coreceptor, capturing an open conformational state in which the fusion machinery on gp41 gains access to the target cell membrane. In the well-characterized closed Env conformation, the gp120 V1V2 loops interact at the apex of the Env trimer. Less is known about the structure of the open CD4-bound state, in which the V1V2 loops must rearrange and separate to allow access to the coreceptor binding site...
October 31, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27798403/a-relaxed-directional-random-walk-model-for-phylogenetic-trait-evolution
#17
Mandev S Gill, Lam Si Tung Ho, Guy Baele, Philippe Lemey, Marc A Suchard
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes...
October 18, 2016: Systematic Biology
https://www.readbyqxmd.com/read/27793589/mapping-out-the-intricate-relationship-of-the-hiv-envelope-protein-and-the-membrane-environment
#18
Yoel A Klug, Etai Rotem, Roland Schwarzer, Yechiel Shai
The HIV gp160 envelope fusion protein is situated in the viral membrane and mediates virus entry into its host cell. Increasing evidence suggests that virtually all parts of the HIV envelope are structurally and functionally dependent on membranes. Protein-lipid interactions and membrane properties influence the dynamics of a manifold of gp160 biological activities such as membrane fusion, immune suppression and gp160 incorporation into virions during HIV budding and assembly. In the following we will summarize our current understanding of this interdependence between membrane interaction, structural conformation and functionality of the different gp160 domains...
October 25, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27793107/acute-hiv-infection-presenting-as-hemophagocytic-syndrome-with-an-unusual-serological-and-virological-response-to-art
#19
Rita Veiga Ferraz, Ana Cláudia Carvalho, Fernando Araújo, Carmo Koch, Cândida Abreu, António Sarmento
BACKGROUND: HIV clinical presentation in the acute stage is variable and some of its virological and immunological aspects are not completely understood. Most cases of HIV- associated reactive hemophagocytic syndrome have been reported in patients with advanced stages of HIV and to our knowledge, there are only 8 cases in the English literature presenting during acute HIV infection, most in East Asia, being this the first case in a European patient. CASE PRESENTATION: We report a case of a European Caucasian 27- year old woman with a primary HIV- infection presenting with extremely low CD4+ T cell count who developed a haemophagocytic syndrome after starting ART and in whom we documented a very unusual serological and virological response, characterized by an impaired HIV- antibody production and a 12 month time frame to reach an undetectable viral load, despite no evidence of resistance...
October 28, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27784796/deconstructing-the-antiviral-neutralizing-antibody-response-implications-for-vaccine-development-and-immunity
#20
REVIEW
Laura A VanBlargan, Leslie Goo, Theodore C Pierson
The antibody response plays a key role in protection against viral infections. While antiviral antibodies may reduce the viral burden via several mechanisms, the ability to directly inhibit (neutralize) infection of cells has been extensively studied. Eliciting a neutralizing-antibody response is a goal of many vaccine development programs and commonly correlates with protection from disease. Considerable insights into the mechanisms of neutralization have been gained from studies of monoclonal antibodies, yet the individual contributions and dynamics of the repertoire of circulating antibody specificities elicited by infection and vaccination are poorly understood on the functional and molecular levels...
December 2016: Microbiology and Molecular Biology Reviews: MMBR
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