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HIV viral dynamics

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https://www.readbyqxmd.com/read/28542550/a-spatio-temporal-assessment-of-simian-human-immunodeficiency-virus-shiv-evolution-reveals-a-highly-dynamic-process-within-the-host
#1
Alison F Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela D M Kashuba, Brandon F Keele, Shiu-Lok Hu, Dmitri A Petrov, Pleuni S Pennings, Zandrea Ambrose
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28540766/hiv-1-full-genome-phylogenetics-of-generalized-epidemics-in-sub-saharan-africa-impact-of-missing-nucleotide-characters-in-next-generation-sequences
#2
Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, M Essex, Simon D W Frost, Astrid Gall, Simani Gaiseitsiwe, Mary Grabowski, Ronald Gray, Stephane Guindon, Arndt von Haeseler, Pontiano Kaleebu, Michelle Kendall, Alexey Kozlov, Justen Manasa, Bui Quang Minh, Sikhulile Moyo, Vladimir Novitsky, Rebecca Nsubuga, Sureshnee Pillay, Thomas C Quinn, David Serwadda, Deogratius Ssemwanga, Alexandros Stamatakis, Jana Trifinopoulos, Maria Wawer, Andrew Leigh Brown, Tulio de Oliveira, Paul Kellam, Deenan Pillay, Christophe Fraser
To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n=2,833; MRC/UVRI Uganda, n=701; Mochudi Prevention Project, n=359; Africa Health Research Institute Resistance Cohort, n=92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai...
May 25, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28539445/structure-of-simian-immunodeficiency-virus-envelope-spikes-bound-with-cd4-and-monoclonal-antibody-36d5
#3
Guiqing Hu, Jun Liu, Kenneth H Roux, Kenneth A Taylor
The HIV-1/SIV envelope spike (Env) mediates the viral entry into host cells. The V3 loop of the gp120 component of the Env trimer contributes to the co-receptor binding site and is a target for neutralizing antibodies. We have used cryoelectron tomography to visualize the binding of CD4 and the V3 loop monoclonal antibody 36D5 to gp120 of the SIV Env. Our results show that 36D5 binds gp120 at the base of the V3 loop and suggest the antibody exerts its neutralization effect by blocking the co-receptor binding site...
May 24, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28531553/hiv-1-viral-load-measurement-in-venous-blood-and-fingerprick-blood-using-abbott-realtime-hiv-1-dbs-assay
#4
Ning Tang, Vihanga Pahalawatta, Andrea Frank, Zowie Bagley, Raquel Viana, John Lampinen, Gregor Leckie, Shihai Huang, Klara Abravaya, Carole L Wallis
BACKGROUND: HIV RNA suppression is a key indicator for monitoring success of antiretroviral therapy. From a logistical perspective, viral load (VL) testing using Dried Blood Spots (DBS) is a promising alternative to plasma based VL testing in resource-limited settings. OBJECTIVES: To evaluate the analytical and clinical performance of the Abbott RealTime HIV-1 assay using a fully automated one-spot DBS sample protocol. STUDY DESIGN: Limit of detection (LOD), linearity, lower limit of quantitation (LLQ), upper limit of quantitation (ULQ), and precision were determined using serial dilutions of HIV-1 Virology Quality Assurance stock (VQA Rush University), or HIV-1-containing armored RNA, made in venous blood...
May 13, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28521720/the-role-of-il-27-and-its-receptor-in-the-pathogenesis-of-hiv-aids-and-anti-viral-immune-response
#5
Yu-Huang Zheng, Shui-Ling Xiao, Bo He, Yan He, Hua-Ying Zhou, Zi Chen, Mei He, Hong-Yan Wang, Yi-He Lin, Jing Cao
BACKGROUND: Cytokines have been widely demonstrated to involve in the pathogenesis of AIDS and the mechanisms of antiretroviral therapy. Interleukin 27 (IL-27) is a new member of the IL-12 cytokine family and has been shown to interfere HIV-1 virus replication with controversial findings. This study is to investigate the dynamic changes in plasma IL-27 level and cell surface IL-27 receptor expression in HIV/AIDS patients who underwent HAART. METHODS: Whole blood was collected from 34 HIV-positive/AIDS patients 0, 6, and 12 months after initiation of HAART and 27 healthy subjects...
May 17, 2017: Current HIV Research
https://www.readbyqxmd.com/read/28515481/conserved-presence-of-g-quadruplex-forming-sequences-in-the-long-terminal-repeat-promoter-of-lentiviruses
#6
Rosalba Perrone, Enrico Lavezzo, Giorgio Palù, Sara N Richter
G-quadruplexes (G4s) are secondary structures of nucleic acids that epigenetically regulate cellular processes. In the human immunodeficiency lentivirus 1 (HIV-1), dynamic G4s are located in the unique viral LTR promoter. Folding of HIV-1 LTR G4s inhibits viral transcription; stabilization by G4 ligands intensifies this effect. Cellular proteins modulate viral transcription by inducing/unfolding LTR G4s. We here expanded our investigation on the presence of LTR G4s to all lentiviruses. G4s in the 5'-LTR U3 region were completely conserved in primate lentiviruses...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28512685/modeling-brain-lentiviral-infections-during-antiretroviral-therapy-in-aids
#7
Weston C Roda, Michael Y Li, Michael S Akinwumi, Eugene L Asahchop, Benjamin B Gelman, Kenneth W Witwer, Christopher Power
Understanding HIV-1 replication and latency in different reservoirs is an ongoing challenge in the care of patients with HIV/AIDS. A mathematical model was created to describe and predict the viral dynamics of HIV-1 and SIV infection within the brain during effective combination antiretroviral therapy (cART). The mathematical model was formulated based on the biology of lentiviral infection of brain macrophages and used to describe the dynamics of transmission and progression of lentiviral infection in brain...
May 16, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/28503119/targeting-hiv-1-envelope-proteins-using-a-fragment-discovery-all-atom-computational-algorithm
#8
Michael H Peters
INTRODUCTION: HIV viral envelope proteins are targets for small inhibitor molecules aimed at disrupting the cellular entry process. Potential peptide-class inhibitor molecules (rDNA drugs) have been previously identified, with mixed results, through biomimicry and phage display experimental methods. Here we describe a new approach based on computational fragment discovery. The method has the potential to not only optimize peptide binding affinity but also to rapidly produce alternative inhibitors against mutated strains...
April 2017: Current Enzyme Inhibition
https://www.readbyqxmd.com/read/28493944/a-decade-of-viral-mutations-and-associated-drug-resistance-in-a-population-of-hiv-1-puerto-ricans-2002-2011
#9
Lycely Del C Sepúlveda-Torres, Lavanya Rishishwar, Maria Luisa Rogers, Eddy Ríos-Olivares, Nawal Boukli, I King Jordan, Luis A Cubano
Puerto Rico has one of the highest rates of HIV/AIDS seen for any US state or territory, and antiretroviral therapy has been a mainstay of efforts to mitigate the HIV/AIDS public health burden on the island. We studied the evolutionary dynamics of HIV-1 mutation and antiretroviral drug resistance in Puerto Rico by monitoring the population frequency of resistance-associated mutations from 2002 to 2011. Whole blood samples from 4,475 patients were analyzed using the TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System in the Immunoretrovirus Research Laboratory at Universidad Central del Caribe...
2017: PloS One
https://www.readbyqxmd.com/read/28489271/successful-treatment-of-kshv-inflammatory-cytokine-syndrome-kics-after-kidney-liver-transplant-correlations-with-hhv8-mirnome-and-specific-t-cell-response
#10
Alessandra Mularoni, Alessia Gallo, Giovanni Riva, Patrizia Barozzi, Monica Miele, Giovanni Cardinale, Giovanni Vizzini, Riccardo Volpes, Paolo Grossi, Daniele Di Carlo, Angelo Luca, Tommaso Trenti, Mario Luppi, Pier Giulio Conaldi
In post-transplant patients, HHV-8/KSHV infection is known to cause aggressive tumors, as well as severe non-neoplastic complications. These latter syndromes are driven by HHV-8/KSHV lytic reactivations and related hyper-inflammatory host responses, typically characterized by high viral loads, elevated levels of cytokines and other inflammation biomarkers, cytopenia, organ failure, high fever, and worsening conditions (with no evidence of B-cell neoplasias). These disorders are associated with a high mortality rate, often due to lack of prompt diagnosis, effective therapeutic approaches, and adequate follow up...
May 10, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28484443/impact-of-genetic-variations-in-hiv-1-tat-on-ltr-mediated-transcription-via-tar-rna-interaction
#11
Larance Ronsard, Nilanjana Ganguli, Vivek K Singh, Kumaravel Mohankumar, Tripti Rai, Subhashree Sridharan, Sankar Pajaniradje, Binod Kumar, Devesh Rai, Suhnrita Chaudhuri, Mohane S Coumar, Vishnampettai G Ramachandran, Akhil C Banerjea
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28472156/genetically-barcoded-siv-facilitates-enumeration-of-rebound-variants-and-estimation-of-reactivation-rates-in-nonhuman-primates-following-interruption-of-suppressive-antiretroviral-therapy
#12
Christine M Fennessey, Mykola Pinkevych, Taina T Immonen, Arnold Reynaldi, Vanessa Venturi, Priyanka Nadella, Carolyn Reid, Laura Newman, Leslie Lipkey, Kelli Oswald, William J Bosche, Matthew T Trivett, Claes Ohlen, David E Ott, Jacob D Estes, Gregory Q Del Prete, Jeffrey D Lifson, Miles P Davenport, Brandon F Keele
HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads. However, this total viral load value represents the sum of many individual infection events, which are difficult to independently track using conventional sequencing approaches. To overcome this challenge, we generated a genetically tagged virus stock (SIVmac239M) with a 34-base genetic barcode inserted between the vpx and vpr accessory genes of the infectious molecular clone SIVmac239. Next-generation sequencing of the virus stock identified at least 9,336 individual barcodes, or clonotypes, with an average genetic distance of 7 bases between any two barcodes...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28466817/dynamic-observation-of-il-33-and-its-receptors-in-hiv-patients-who-received-haart
#13
B He, L Zheng, H Zhou, Y He, Z Chen, S Xiao, H Wang, Y Ling, Y Zheng
The purpose of this study was to observe the changes in serum IL-33 and its soluble receptors, serum sST2 level and ST2L expression in PBMCs of HIV-infected patients receiving highly-active antiretroviral therapy (HAART) for 12 monthes. Fifty-five chronic HIV-1-infected adults were recruited for this study before initiation of HAART. 30 age and gender matched healthy adults were recruited as control. Blood was obtained from each patient at baseline (0 month) and 12 months after initiation of highly active antiretroviral therapy(HAART), and each healthy person...
March 31, 2017: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28457706/a-versatile-tool-for-live-cell-imaging-and-super-resolution-nanoscopy-studies-of-hiv-1-env-distribution-and-mobility
#14
Volkan Sakin, Janina Hanne, Jessica Dunder, Maria Anders-Össwein, Vibor Laketa, Ivana Nikić, Hans-Georg Kräusslich, Edward A Lemke, Barbara Müller
The envelope glycoproteins (Env) of HIV-1 mediate cell entry through fusion of the viral envelope with a target cell membrane. Intramembrane mobility and clustering of Env trimers at the viral budding site are essential for its function. Previous live-cell and super-resolution microscopy studies were limited by lack of a functional fluorescent Env derivative, requiring antibody labeling for detection. Introduction of a bio-orthogonal amino acid by genetic code expansion, combined with click chemistry, offers novel possibilities for site-specific, minimally invasive labeling...
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28431573/a-highly-pathogenic-simian-human-immunodeficiency-virus-effectively-produces-infectious-virions-compared-with-a-less-pathogenic-virus-in-cell-culture
#15
Shoya Iwanami, Yusuke Kakizoe, Satoru Morita, Tomoyuki Miura, Shinji Nakaoka, Shingo Iwami
BACKGROUND: The host range of human immunodeficiency virus (HIV) is quite narrow. Therefore, analyzing HIV-1 pathogenesis in vivo has been limited owing to lack of appropriate animal model systems. To overcome this, chimeric simian and human immunodeficiency viruses (SHIVs) that encode HIV-1 Env and are infectious to macaques have been developed and used to investigate the pathogenicity of HIV-1 in vivo. So far, we have many SHIV strains that show different pathogenesis in macaque experiments...
April 21, 2017: Theoretical Biology & Medical Modelling
https://www.readbyqxmd.com/read/28423342/a-broadly-neutralizing-antibody-targets-the-dynamic-hiv-envelope-trimer-apex-via-a-long-rigidified-and-anionic-%C3%AE-hairpin-structure
#16
Jeong Hyun Lee, Raiees Andrabi, Ching-Yao Su, Anila Yasmeen, Jean-Philippe Julien, Leopold Kong, Nicholas C Wu, Ryan McBride, Devin Sok, Matthias Pauthner, Christopher A Cottrell, Travis Nieusma, Claudia Blattner, James C Paulson, Per Johan Klasse, Ian A Wilson, Dennis R Burton, Andrew B Ward
Broadly neutralizing antibodies (bnAbs) to HIV delineate vaccine targets and are prophylactic and therapeutic agents. Some of the most potent bnAbs target a quaternary epitope at the apex of the surface HIV envelope (Env) trimer. Using cryo-electron microscopy, we solved the atomic structure of an apex bnAb, PGT145, in complex with Env. We showed that the long anionic HCDR3 of PGT145 penetrated between glycans at the trimer 3-fold axis, to contact peptide residues from all three Env protomers, and thus explains its highly trimer-specific nature...
April 18, 2017: Immunity
https://www.readbyqxmd.com/read/28422752/t-bet-b-cells-are-induced-by-human-viral-infections-and-dominate-the-hiv-gp140-response
#17
James J Knox, Marcus Buggert, Lela Kardava, Kelly E Seaton, Michael A Eller, David H Canaday, Merlin L Robb, Mario A Ostrowski, Steven G Deeks, Mark K Slifka, Georgia D Tomaras, Susan Moir, M Anthony Moody, Michael R Betts
Humoral immunity is critical for viral control, but the identity and mechanisms regulating human antiviral B cells are unclear. Here, we characterized human B cells expressing T-bet and analyzed their dynamics during viral infections. T-bet+ B cells demonstrated an activated phenotype, a distinct transcriptional profile, and were enriched for expression of the antiviral immunoglobulin isotypes IgG1 and IgG3. T-bet+ B cells expanded following yellow fever virus and vaccinia virus vaccinations and also during early acute HIV infection...
April 20, 2017: JCI Insight
https://www.readbyqxmd.com/read/28416550/identification-and-optimization-of-thienopyridine-carboxamides-as-inhibitors-of-hiv-regulatory-complexes
#18
Robert L Nakamura, Mark A Burlingame, Shumin Yang, David C Crosby, Dale J Talbot, Kitty Chui, Alan D Frankel, Adam R Renslo
Viral regulatory complexes perform critical functions during virus replication and are important targets for therapeutic intervention. In HIV, the Tat and Rev proteins form complexes with multiple viral and cellular factors to direct transcription and export of the viral RNA. These complexes are composed of many proteins and are dynamic, making them difficult to fully recapitulate in vitro Therefore we developed a cell-based reporter assay to monitor the assembly of viral complexes for inhibitor screening. We screened a small molecule library and identified multiple hits that inhibit the activity of the viral complexes...
April 17, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28411091/comparison-of-dynamic-monitoring-strategies-based-on-cd4-cell-counts-in-virally-suppressed-hiv-positive-individuals-on-combination-antiretroviral-therapy-in-high-income-countries-a-prospective-observational-study
#19
Ellen C Caniglia, Lauren E Cain, Caroline A Sabin, James M Robins, Roger Logan, Sophie Abgrall, Michael J Mugavero, Sonia Hernández-Díaz, Laurence Meyer, Remonie Seng, Daniel R Drozd, George R Seage, Fabrice Bonnet, Francois Dabis, Richard D Moore, Peter Reiss, Ard van Sighem, William C Mathews, Julia Del Amo, Santiago Moreno, Steven G Deeks, Roberto Muga, Stephen L Boswell, Elena Ferrer, Joseph J Eron, Sonia Napravnik, Sophie Jose, Andrew Phillips, Amy C Justice, Janet P Tate, John Gill, Antonio Pacheco, Valdilea G Veloso, Heiner C Bucher, Matthias Egger, Hansjakob Furrer, Kholoud Porter, Giota Touloumi, Heidi Crane, Jose M Miro, Jonathan A Sterne, Dominique Costagliola, Michael Saag, Miguel A Hernán
BACKGROUND: Clinical guidelines vary with respect to the optimal monitoring frequency of HIV-positive individuals. We compared dynamic monitoring strategies based on time-varying CD4 cell counts in virologically suppressed HIV-positive individuals. METHODS: In this observational study, we used data from prospective studies of HIV-positive individuals in Europe (France, Greece, the Netherlands, Spain, Switzerland, and the UK) and North and South America (Brazil, Canada, and the USA) in The HIV-CAUSAL Collaboration and The Centers for AIDS Research Network of Integrated Clinical Systems...
April 11, 2017: Lancet HIV
https://www.readbyqxmd.com/read/28404854/autologous-stem-cell-transplantation-disrupts-adaptive-immune-responses-during-rebound-shiv-viremia
#20
Daniel B Reeves, Christopher W Peterson, Hans-Peter Kiem, Joshua T Schiffer
Primary HIV-1 infection induces a virus-specific adaptive/cytolytic immune response that impacts plasma viral load setpoint and rate of progression to AIDS. Combination antiretroviral therapy (cART) suppresses plasma viremia to undetectable levels that rebound upon cART treatment interruption. Following cART withdrawal, the memory component of the virus-specific adaptive immune response may improve viral control compared to primary infection. Here, using primary infection and treatment interruption data from macaques infected with simian/human immunodeficiency virus (SHIV), we observe lower peak viral load but unchanged viral setpoint during viral rebound...
April 12, 2017: Journal of Virology
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