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HIV evolution

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https://www.readbyqxmd.com/read/28333353/evolution-of-blood-associated-hiv-1-dna-levels-after-48-weeks-of-switching-to-atazanavir-ritonavir-lamivudine-dual-therapy-versus-continuing-triple-therapy-in-the-randomized-atlas-m-trial
#1
Francesca Lombardi, Simone Belmonti, Eugenia Quiros-Roldan, Alessandra Latini, Antonella Castagna, Gabriella D'Ettorre, Roberta Gagliardini, Massimiliano Fabbiani, Roberto Cauda, Andrea De Luca, Simona Di Giambenedetto
Objectives: The AtLaS-M randomized trial showed that in patients with HIV-1 RNA <50 copies/mL on atazanavir/ritonavir + two NRTIs, switching to a dual therapy with atazanavir/ritonavir+lamivudine had superior efficacy as compared with continuing the previous triple therapy. This substudy was designed to evaluate at 48 weeks the impact of the dual therapy versus the three-drug atazanavir/ritonavir-based therapy on the HIV-1 cellular reservoir as reflected by the quantification of blood-associated HIV-1 DNA levels...
March 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28332348/molecular-epidemiology-of-hiv
#2
REVIEW
Bum Sik Chin
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea...
March 22, 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/28332090/disparities-in-the-clinical-evolution-of-anal-neoplasia-in-an-hiv-infected-cohort
#3
Edward R Cachay, Wollelaw Agmas, Wm Christopher Mathews
BACKGROUND: A recent meta-analysis suggested that anal intraepithelial neoplasia and invasive anal cancer are more prevalent among black men having sex with men (MSM). METHODS: We conducted a retrospective cohort of HIV-infected adult patients under care between 2001 and 2012. Disparities in clinical evolution of anal intraepithelial neoplasia to high-grade squamous intraepithelial lesion (HSIL) and invasive anal cancer were evaluated in a three-state Markov model adjusted for cytology misclassification...
March 23, 2017: Journal of Racial and Ethnic Health Disparities
https://www.readbyqxmd.com/read/28331087/feline-immunodeficiency-virus-evolutionarily-acquires-two-proteins-vif-and-protease-capable-of-antagonizing-feline-apobec3
#4
Rokusuke Yoshikawa, Junko S Takeuchi, Eri Yamada, Yusuke Nakano, Naoko Misawa, Yuichi Kimura, Fengrong Ren, Takayuki Miyazawa, Yoshio Koyanagi, Kei Sato
The interplay between viral and host proteins has been well studied to elucidate virus-host interactions and their relevance to virulence. Mammalian genes encode apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins, which act as intrinsic restriction factors against lentiviruses. To overcome APOBEC3-mediated anti-viral actions, lentiviruses have evolutionarily acquired an accessory protein, viral infectivity factor (Vif), and Vif degrades host APOBEC3 proteins via a ubiquitin/proteasome-dependent pathway...
March 22, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28328797/activation-senescence-and-inflammation-markers-in-hiv-patients-association-with-renal-function
#5
Alexandra Ozanne, Pierre Duffau, Frédéric-Antoine Dauchy, Claire Rigothier, Cécile Terrien, Estibaliz Lazaro, Charles Cazanave, Sylvie Lawson-Ayayi, Fabrice Bonnet, Patrick Blanco, Linda Wittkop, Isabelle Pellegrin
OBJECTIVES: To assess the association between immune-activation (IA), immune-senescence (IS), inflammation biomarkers and renal function measured by estimated glomerular function rate (eGFR) at inclusion and its evolution over a 3-years follow-up in HIV-infected patients with undetectable viral load. DESIGN: The CIADIS (Chronic Immune Activation anD Senescence) sub-study consecutively included patients between October 2011 and May 2013 enrolled in the ANRS CO3 Aquitaine observational cohort...
March 21, 2017: AIDS
https://www.readbyqxmd.com/read/28323897/hcv-coinfection-contributes-to-hiv-pathogenesis-by-increasing-immune-exhaustion-in-cd8-t-cells
#6
Norma Rallón, Marcial García, Javier García-Samaniego, Noelia Rodríguez, Alfonso Cabello, Clara Restrepo, Beatriz Álvarez, Rosa García, Miguel Górgolas, José M Benito
BACKGROUND: There are several contributors to HIV-pathogenesis or insufficient control of the infection. However, whether HIV/HCV-coinfected population exhibits worst evolution of HIV-pathogenesis remains unclear. Recently, some markers of immune exhaustion have been proposed as preferentially upregulated on T-cells during HIV-infection. Herein, we have analyzed T-cell exhaustion together with several other contributors to HIV-pathogenesis that could be affected by HCV-coinfection. PATIENTS AND METHODS: Ninety-six patients with chronic HIV-infection (60 HIV-monoinfected and 36 HIV/HCV-coinfected), and 20 healthy controls were included in the study...
2017: PloS One
https://www.readbyqxmd.com/read/28275446/evolution-of-the-health-sector-response-to-hiv-in-myanmar-progress-challenges-and-the-way-forward
#7
EDITORIAL
Htun Nyunt Oo, San Hone, Masami Fujita, Amaya Maw-Naing, Krittayawan Boonto, Marjolein Jacobs, Sabe Phyu, Phavady Bollen, Jacquie Cheung, Htin Aung, May Thu Aung Sang, Aye Myat Soe, Razia Pendse, Eamonn Murphy
Critical building blocks for the response to HIV were made until 2012 despite a series of political, social and financial challenges. A rapid increase of HIV service coverage was observed from 2012 to 2015 through collaborative efforts of government and non-governmental organisations (NGOs). Government facilities, in particular, demonstrated their capacity to expand services for antiretroviral therapy (ART), prevention of mother-to-child transmission (PMTCT) of HIV, tuberculosis and HIV co-infection and methadone-maintenance therapy (MMT)...
November 28, 2016: Journal of Virus Eradication
https://www.readbyqxmd.com/read/28275184/rna-associated-early-stage-anti-viral-factor-reaf-is-a-major-component-of-lv2-restriction
#8
Kelly M Marno, Eithne O'Sullivan, Christopher E Jones, Julieta Díaz-Delfín, Claire Pardieu, Richard D Sloan, Áine McKnight
HIV and SIV replication in human cells is restricted at early post-entry steps by host inhibitory factors. We previously described and characterised an early phase restriction of HIV-1 and 2 replication in human cell lines, primary macrophages and PBMCs. The restriction was termed Lentiviral restriction 2 (Lv2). The viral determinants of Lv2 susceptibility mapped to the HIV-2 Env and CA. We subsequently reported a whole genome siRNA screen for factors involved in to HIV which identified RNA-associated Early-stage Anti-viral Factor (REAF)...
March 8, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28264054/delineating-cd4-dependency-of-hiv-1-adaptation-to-infect-low-level-cd4-expressing-target-cells-widens-cellular-tropism-but-severely-impacts-on-envelope-functionality
#9
David Beauparlant, Peter Rusert, Carsten Magnus, Claus Kadelka, Jacqueline Weber, Therese Uhr, Osvaldo Zagordi, Corinna Oberle, Maria J Duenas-Decamp, Paul R Clapham, Karin J Metzner, Huldrych F Günthard, Alexandra Trkola
A hallmark of HIV-1 infection is the continuously declining number of the virus' predominant target cells, activated CD4+ T cells. With diminishing CD4+ T cell levels, the capacity to utilize alternate cell types and receptors, including cells that express low CD4 receptor levels such as macrophages, thus becomes crucial. To explore evolutionary paths that allow HIV-1 to acquire a wider host cell range by infecting cells with lower CD4 levels, we dissected the evolution of the envelope-CD4 interaction under in vitro culture conditions that mimicked the decline of CD4high target cells, using a prototypic subtype B, R5-tropic strain...
March 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28264037/cognitive-change-trajectories-in-virally-suppressed-hiv-infected-individuals-indicate-high-prevalence-of-disease-activity
#10
Chloe Gott, Thomas Gates, Nadene Dermody, Bruce J Brew, Lucette A Cysique
BACKGROUND: The longitudinal rate and profile of cognitive decline in persons with stable, treated, and virally suppressed HIV infection is not established. To address this question, the current study quantifies the rate of cognitive decline in a cohort of virally suppressed HIV+ persons using clinically relevant definitions of decline, and determine cognitive trajectories taking into account historical and baseline HAND status. METHODS: Ninety-six HIV+ (clinically stable and virally undetectable) and 44 demographically comparable HIV- participants underwent standard neuropsychological testing at baseline and 18-months follow-up...
2017: PloS One
https://www.readbyqxmd.com/read/28250813/modelling-the-evolution-of-hiv-1-virulence-in-response-to-imperfect-therapy-and-prophylaxis
#11
David R M Smith, Nicole Mideo
Average HIV-1 virulence appears to have evolved in different directions in different host populations since antiretroviral therapy first became available, and models predict that HIV drugs can select for either higher or lower virulence, depending on how treatment is administered. However, HIV virulence evolution in response to "leaky" therapy (treatment that imperfectly suppresses viral replication) and the use of preventive drugs (pre-exposure prophylaxis) has not been explored. Using adaptive dynamics, we show that higher virulence can evolve when antiretroviral therapy is imperfectly effective and that this evolution erodes some of the long-term clinical and epidemiological benefits of HIV treatment...
March 2017: Evolutionary Applications
https://www.readbyqxmd.com/read/28220254/hiv-1-persistent-viremia-is-frequently-followed-by-episodes-of-low-level-viremia
#12
Marek Widera, Miriam Dirks, Barbara Bleekmann, Robert Jablonka, Martin Däumer, Hauke Walter, Robert Ehret, Jens Verheyen, Stefan Esser
After the start of antiretroviral therapy (ART), plasma HIV-RNA levels should fall below the limit of detection (LOD) within 24 weeks. Hence, the prolonged decline of HIV-RNA after ART initiation is defined as persistent viremia (PV). In this retrospective study, we analyzed factors associated with PV. Next-generation sequencing of viral RNA/DNA was performed to study viral evolution and the emergence of drug-resistance mutations in HIV-infected patients with PV (n = 20). In addition, HIV-DNA species, immunological parameters, and clinical data of the patients were analyzed...
February 20, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28220205/global-properties-of-nested-network-model-with-application-to-multi-epitope-hiv-ctl-dynamics
#13
Cameron Browne
Mathematical modeling and analysis can provide insight on the dynamics of ecosystems which maintain biodiversity in the face of competitive and prey-predator interactions. Of primary interests are the underlying structure and features which stabilize diverse ecological networks. Recently Korytowski and Smith (Theor Ecol 8(1):111-120, 2015) proved that a perfectly nested infection network, along with appropriate life history trade-offs, leads to coexistence and persistence of bacteria-phage communities in a chemostat model...
February 20, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28219520/erratum-to-editorial-for-special-issue-on-evolution-of-hiv-infect-genet-evol-vol-46-december-2016-pp-149
#14
A Ayouba, D Paraskevis, M Peeters
No abstract text is available yet for this article.
March 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28207500/strategic-use-of-dual-regimens-of-boosted-protease-inhibitors-plus-maraviroc-in-poorly-adherent-subjects-in-view-of-long-acting-drugs-a-retrospective-study
#15
Amedeo Ferdinando Capetti, Mariangela Micale, Laura Carenzi, Fosca Niero, Simona Landonio, Stefania Vimercati, Gianfranco Dedivitiis, Giuliano Rizzardini
In view of the forthcoming long-acting antiretrovirals, measures should be taken to prevent the selection of HIV drug resistance mutations. All subjects who had been switched to boosted protease inhibitors plus maraviroc (bPIs/MVC) with baseline HIV-1 RNA >50 copies/mL between June, 2014, and April, 2015, were retrospectively evaluated. HIV-1 RNA, CD4+ T-cells, serum glucose, creatinine, ALT, and adverse events were controlled every 3 to 4 months. We retrospectively analyzed 44 patients: 18 were taking darunavir/ritonavir (DRV/r) and 26 atazanavir/ritonavir (ATV/r) once daily, plus MVC 300 mg once daily...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28193894/rules-of-rna-specificity-of-hnrnp-a1-revealed-by-global-and-quantitative-analysis-of-its-affinity-distribution
#16
Niyati Jain, Hsuan-Chun Lin, Christopher E Morgan, Michael E Harris, Blanton S Tolbert
Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a multipurpose RNA-binding protein (RBP) involved in normal and pathological RNA metabolism. Transcriptome-wide mapping and in vitro evolution identify consensus hnRNP A1 binding motifs; however, such data do not reveal how surrounding RNA sequence and structural context modulate affinity. We determined the affinity of hnRNP A1 for all possible sequence variants (n = 16,384) of the HIV exon splicing silencer 3 (ESS3) 7-nt apical loop. Analysis of the affinity distribution identifies the optimal motif 5'-YAG-3' and shows how its copy number, position in the loop, and loop structure modulate affinity...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28190897/synthesis-of-multivalent-glycopeptide-conjugates-that-mimic-an-hiv-epitope
#17
Jennifer K Bailey, Dung N Nguyen, Satoru Horiya, Isaac J Krauss
Recently, we reported a directed evolution method which enabled us to discover sequences of glycopeptides that bind with picomolar affinity to HIV antibody 2G12 and are of interest as HIV vaccine candidates. In this manuscript, we describe the syntheses of several of these large (~11-12 kDa) glycopeptides by a combination of fast flow peptide synthesis and click chemistry. We also discuss the optimization of their attachment to carrier protein CRM197, affording antigenic and immunogenic conjugates ready for animal vaccination...
October 6, 2016: Tetrahedron
https://www.readbyqxmd.com/read/28188180/a-population-genomics-approach-to-assessing-the-genetic-basis-of-within-host-microevolution-underlying-recurrent-cryptococcal-meningitis-infection
#18
Johanna Rhodes, Mathew A Beale, Mathieu Vanhove, Joseph N Jarvis, Shichina Kannambath, John A Simpson, Anthea Ryan, Graeme Meintjes, Thomas S Harrison, Matthew C Fisher, Tihana Bicanic
Recurrence of meningitis due to Cryptococcus neoformans after treatment causes substantial mortality in HIV/AIDS patients across sub-Saharan Africa. In order to determine whether recurrence occurred due to relapse of the original infecting isolate or reinfection with a different isolate weeks or months after initial treatment, we used whole-genome sequencing to assess the genetic basis of infection in 17 HIV-infected individuals with recurrent cryptococcal meningitis. Comparisons revealed a clonal relationship for 15 pairs of isolates recovered before and after recurrence showing relapse of the original infection...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28187688/identification-of-a-novel-hiv-type-1-recombinant-form-crf01_ae-crf07_bc-in-men-who-have-sex-with-men-in-zhejiang-china
#19
Yufan Xu, Xiaorong Peng, Tiansheng Xie, Xiangyun Lu, Nanping Wu
The prevalence of HIV-1 is increasing rapidly among the population of men who have sex with men (MSM) in China. Here, we report a novel HIV type 1 recombinant form consisting of CRF01_AE and CRF07_BC detected in a male patient through homosexual behavior. A phylogenic analysis revealed that this unique recombinant form (URF) exhibits a complex genomic structure with three CRF07_BC regions inserted into the CRF01_AE backbone. Recently, several second-generation recombinant forms (e.g., CRF01_AE/CRF07_BC) have been identified among MSM in China...
February 10, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28182609/genetic-polymorphisms-associated-with-liver-disease-progression-in-hiv-hcv-coinfected-patients
#20
REVIEW
Luz M Medrano, María A Jiménez-Sousa, Amanda Fernández-Rodríguez, Salvador Resino
The pathogenic mechanisms of the accelerated progression of liver injury in HIV/HCV coinfection are incompletely understood. The progression of liver disease is variable between individuals having similar risk factors, suggesting that genetic background is an important contributor. The aim of this review is to give a summary of all single nucleotide polymorphisms associated with the severity of liver disease in patients coinfected with HIV and HCV reported in the literature. Therefore, a systematic search for articles published was made, 17 of which were selected for this review...
January 2017: AIDS Reviews
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