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HIV bioinformatics

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https://www.readbyqxmd.com/read/28287540/silac-based-proteomic-characterization-of-exosomes-from-hiv-1-infected-cells
#1
Collins Cheruiyot, Zemplen Pataki, Robert Williams, Bharat Ramratnam, Ming Li
Proteomics is the large-scale analysis of proteins. Proteomic techniques, such as liquid chromatography tandem mass spectroscopy (LC-MS/MS), can characterize thousands of proteins at a time. These powerful techniques allow us to have a systemic understanding of cellular changes, especially when cells are subjected to various stimuli, such as infections, stresses, and specific test conditions. Even with recent developments, analyzing the exosomal proteome is time-consuming and often involves complex methodologies...
March 3, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28239376/a-mature-nk-profile-at-the-time-of-hiv-primary-infection-is-associated-with-an-early-response-to-cart
#2
Françoise Gondois-Rey, Antoine Chéret, Françoise Mallet, Ghislain Bidaut, Samuel Granjeaud, Camille Lécuroux, Mickaël Ploquin, Michaela Müller-Trutwin, Christine Rouzioux, Véronique Avettand-Fenoël, Andrea De Maria, Gilles Pialoux, Cécile Goujard, Laurence Meyer, Daniel Olive
Natural killer (NK) cells are major effectors of the innate immune response. Despite an overall defect in their function associated with chronic human immunodeficiency virus (HIV) infection, their role in primary HIV infection is poorly understood. We investigated the modifications of the NK cell compartment in patients from the ANRS-147-Optiprim trial, a study designed to examine the benefits of intensive combination antiretroviral therapy (cART) in patients with acute or early primary HIV infection. Multiparametric flow cytometry combined with bioinformatics analyses identified the NK phenotypes in blood samples from 30 primary HIV-infected patients collected at inclusion and after 3 months of cART...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28187204/differentiating-founder-and-chronic-hiv-envelope-sequences
#3
John M Murray, Stephen Maher, Talia Mota, Kazuo Suzuki, Anthony D Kelleher, Rob J Center, Damian Purcell
Significant progress has been made in characterizing broadly neutralizing antibodies against the HIV envelope glycoprotein Env, but an effective vaccine has proven elusive. Vaccine development would be facilitated if common features of early founder virus required for transmission could be identified. Here we employ a combination of bioinformatic and operations research methods to determine the most prevalent features that distinguish 78 subtype B and 55 subtype C founder Env sequences from an equal number of chronic sequences...
2017: PloS One
https://www.readbyqxmd.com/read/28182621/primary-hiv-1-drug-resistant-minority-variants
#4
Benjamin Chimukangara, Reshmi Samuel, Kogieleum Naidoo, Tulio de Oliveira
Primary HIV drug resistant mutations are mutations that occur in an HIV-infected individual prior to the initiation of antiretroviral therapy (ART). These mutations may arise by de novo mutagenesis or result from transmission. Drug resistant mutations (DRMs) may reduce the effectiveness of ART leading to inadequate virological outcomes. Currently, Sanger sequencing is the standard method for detection of DRMs to inform treatment decisions, but does not detect minor variant mutations. Drug resistant minority variants (DRMVs) can be detected by next generation sequencing (NGS)...
February 9, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28182618/the-evolving-landscape-of-hiv-drug-resistance-diagnostics-for-expanding-testing-in-resource-limited-settings
#5
Seth C Inzaule, Raph L Hamers, Roger Paredes, Chunfu Yang, Rob Schuurman, Tobias F Rinke de Wit
Global scale-up of antiretroviral treatment (ART) has dramatically changed the prospects of HIV/AIDS disease rendering life-long chronic care and treatment a reality for millions of HIV-infected patients. Affordable technologies to monitor ART are needed to ensure long-term durability of limited available drug regimens. HIV drug resistance tests can complement existing strategies in optimizing clinical decision-making for patients with treatment failure, in addition to facilitating population-based surveillance of HIV drug resistance...
February 9, 2017: AIDS Reviews
https://www.readbyqxmd.com/read/28177783/expression-purification-and-renaturation-of-recombinant-peptide-based-hiv-vaccine-in-escherichia-coli
#6
Wei He, Jiayi Shu, Jian Zhang, Zhihua Liu, Jianqing Xu, Xia Jin, Xuedong Wang
One of the new HIV vaccine strategies is to design epitope-based immunogen. We previously predicted 20 potential HIV epitopes using bioinformatics approaches. The combination of these 20 epitopes has a theoretical coverage of 98.1% of the population for both the prevalent HIV genotypes and Chinese human leukocyte antigen (HLA) DR types. In order to test whether this vaccine is immunogenic in vivo, a corresponding antigen needs to be prepared. To this end, we constructed recombinant plasmid containing DNA encoding 300 amino acids of this vaccine protein, and then transformed Escherichia coli BL21 (DE3) cells with the plasmid...
January 27, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28133812/antibodyomics-bioinformatics-technologies-for-understanding-b-cell-immunity-to-hiv-1
#7
REVIEW
Peter D Kwong, Gwo-Yu Chuang, Brandon J DeKosky, Tatyana Gindin, Ivelin S Georgiev, Thomas Lemmin, Chaim A Schramm, Zizhang Sheng, Cinque Soto, An-Suei Yang, John R Mascola, Lawrence Shapiro
Numerous antibodies have been identified from HIV-1-infected donors that neutralize diverse strains of HIV-1. These antibodies may provide the basis for a B cell-mediated HIV-1 vaccine. However, it has been unclear how to elicit similar antibodies by vaccination. To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies. As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway, and prevalence of broadly neutralizing antibody lineages (Antibodyomics1, 2, 4, and 6)...
January 2017: Immunological Reviews
https://www.readbyqxmd.com/read/28110145/virusseeker-a-computational-pipeline-for-virus-discovery-and-virome-composition-analysis
#8
Guoyan Zhao, Guang Wu, Efrem S Lim, Lindsay Droit, Siddharth Krishnamurthy, Dan H Barouch, Herbert W Virgin, David Wang
The advent of Next Generation Sequencing (NGS) has vastly increased our ability to discover novel viruses and to systematically define the spectrum of viruses present in a given specimen. Such studies have led to the discovery of novel viral pathogens as well as broader associations of the virome with diverse diseases including inflammatory bowel disease, severe acute malnutrition and HIV/AIDS. Critical to the success of these efforts are robust bioinformatic pipelines for rapid classification of microbial sequences...
March 2017: Virology
https://www.readbyqxmd.com/read/28099515/polymorphisms-and-mutational-covariation-associated-with-death-in-a-prospective-cohort-of-hiv-aids-patients-receiving-long-term-art-in-china
#9
Pengtao Liu, Yi Feng, Jianjun Wu, Suian Tian, Bin Su, Zhe Wang, Lingjie Liao, Hui Xing, Yinghui You, Yiming Shao, Yuhua Ruan
BACKGROUND: HIV drug resistance is associated with faster clinical progression of AIDS. However, the effect of significant polymorphisms and mutational covariation on mortality among HIV/AIDS patients receiving long-term antiretroviral therapy (ART), have rarely been studied. METHODS: In this prospective cohort study from December 2003 to December 2014, we present a new computational modelling approach based on bioinformatics-based models and several statistical methods to elucidate the molecular mechanisms involved in the acquisition of polymorphisms and mutations on death in HIV/AIDS patients receiving long-term ART in China...
2017: PloS One
https://www.readbyqxmd.com/read/28086981/does-antiretroviral-treatment-change-hiv-1-codon-usage-patterns-in-its-genes-a-preliminary-bioinformatics-study
#10
Navaneethan Palanisamy, Nathan Osman, Frédéric Ohnona, Hong-Tao Xu, Bluma Brenner, Thibault Mesplède, Mark A Wainberg
BACKGROUND: Codon usage bias has been described for various organisms and is thought to contribute to the regulation of numerous biological processes including viral infections. HIV-1 codon usage has been previously shown to be different from that of other viruses and man. It is evident that the antiretroviral drugs used to restrict HIV-1 replication also select for resistance variants. We wanted to test whether codon frequencies in HIV-1 sequences from treatment-experienced patients differ from those of treatment-naive individuals due to drug pressure affecting codon usage bias...
January 7, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27999055/unravelling-the-dynamics-of-selection-of-multiresistant-variants-to-integrase-inhibitors-in-an-hiv-1-infected-child-using-ultra-deep-sequencing
#11
Karl Stefic, Maud Salmona, Marisa Capitao, Marion Splittgerber, Zoha Maakaroun-Vermesse, Marie-Laure Néré, Louis Bernard, Marie-Laure Chaix, Francis Barin, Constance Delaugerre
BACKGROUND: Ultra-deep sequencing (UDS) allows detection of minority resistant variants (MRVs) with a threshold of 1% and could be useful to identify variants harbouring single or multiple drug-resistance mutations (DRMs). OBJECTIVES: We analysed the integrase gene region longitudinally using UDS in an HIV-1-infected child rapidly failing a raltegravir-based regimen. METHODS: Longitudinal plasma samples at baseline and weeks 4, 8, 13, 17 and 39 were obtained, as well as the mother's baseline plasma sample...
December 20, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27964762/new-tools-to-analyze-overlapping-coding-regions
#12
Amir H Bayegan, Juan Antonio Garcia-Martin, Peter Clote
BACKGROUND: Retroviruses transcribe messenger RNA for the overlapping Gag and Gag-Pol polyproteins, by using a programmed -1 ribosomal frameshift which requires a slippery sequence and an immediate downstream stem-loop secondary structure, together called frameshift stimulating signal (FSS). It follows that the molecular evolution of this genomic region of HIV-1 is highly constrained, since the retroviral genome must contain a slippery sequence (sequence constraint), code appropriate peptides in reading frames 0 and 1 (coding requirements), and form a thermodynamically stable stem-loop secondary structure (structure requirement)...
December 13, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27959928/an-efficient-microarray-based-genotyping-platform-for-the-identification-of-drug-resistance-mutations-in-majority-and-minority-subpopulations-of-hiv-1-quasispecies
#13
Verónica Martín, Celia Perales, María Fernández-Algar, Helena G Dos Santos, Patricia Garrido, María Pernas, Víctor Parro, Miguel Moreno, Javier García-Pérez, José Alcamí, José Luis Torán, David Abia, Esteban Domingo, Carlos Briones
The response of human immunodeficiency virus type 1 (HIV-1) quasispecies to antiretroviral therapy is influenced by the ensemble of mutants that composes the evolving population. Low-abundance subpopulations within HIV-1 quasispecies may determine the viral response to the administered drug combinations. However, routine sequencing assays available to clinical laboratories do not recognize HIV-1 minority variants representing less than 25% of the population. Although several alternative and more sensitive genotyping techniques have been developed, including next-generation sequencing (NGS) methods, they are usually very time consuming, expensive and require highly trained personnel, thus becoming unrealistic approaches in daily clinical practice...
2016: PloS One
https://www.readbyqxmd.com/read/27867045/minvar-a-rapid-and-versatile-tool-for-hiv-1-drug-resistance-genotyping-by-deep-sequencing
#14
Michael Huber, Karin J Metzner, Fabienne D Geissberger, Cyril Shah, Christine Leemann, Thomas Klimkait, Jürg Böni, Alexandra Trkola, Osvaldo Zagordi
Genotypic monitoring of drug-resistance mutations (DRMs) in HIV-1 infected individuals is strongly recommended to guide selection of the initial antiretroviral therapy (ART) and changes of drug regimens. Traditionally, mutations conferring drug resistance are detected by population sequencing of the reverse transcribed viral RNA encoding the HIV-1 enzymes target by ART, followed by manual analysis and interpretation of Sanger sequencing traces. This process is labor intensive, relies on subjective interpretation from the operator, and offers limited sensitivity as only mutations above 20% frequency can be reliably detected...
February 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/27818211/deep-sequencing-for-hiv-1-clinical-management
#15
REVIEW
Maria Casadellà, Roger Paredes
The emerging HIV-1 resistance epidemic is threatening the impressive global advances in HIV-1 infection treatment and prevention achieved in the last decade. Next-generation sequencing is improving our ability to understand, diagnose and prevent HIV-1 resistance, being increasingly cost-effective and more accessible. However, NGS still faces a number of limitations that need to be addressed to enable its widespread use. Here, we will review the main NGS platforms available for HIV-1 diagnosis, the factors affecting the clinical utility of NGS testing and the evidence supporting -or not- ultrasensitive genotyping over Sanger sequencing for routine HIV-1 diagnosis...
November 3, 2016: Virus Research
https://www.readbyqxmd.com/read/27662407/modeling-hiv-vaccine-trials-of-the-future
#16
Peter B Gilbert, Ying Huang, Holly E Janes
PURPOSE OF REVIEW: Models of implementation of known-effective interventions for HIV prevention indicate that an efficacious vaccine to prevent HIV infection would be critical for controlling the HIV pandemic. Key issues in the design of future HIV vaccine trials are: first, how to develop reliable immunological correlates of vaccine efficacy, second, how to down-select candidate vaccine regimens into efficacy trials, and third, how to learn about vaccine efficacy in the context of the evolving HIV prevention landscape...
November 2016: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/27605599/structural-equation-modelling-of-viral-tropism-reveals-its-impact-on-achieving-viral-suppression-within-6-months-in-treatment-naive-hiv-1-infected-patients-after-combination-antiretroviral-therapy
#17
Carlo Mengoli, Samantha Andreis, Renzo Scaggiante, Mario Cruciani, Oliviero Bosco, Roberto Ferretto, Davide Leoni, Gaetano Maffongelli, Monica Basso, Carlo Torti, Loredana Sarmati, Massimo Andreoni, Giorgio Palù, Saverio Giuseppe Parisi
OBJECTIVES: To evaluate the role of pre-treatment co-receptor tropism of plasma HIV on the achievement of viral suppression (plasma HIV RNA 1.69 log10 copies/mL) at the sixth month of combination antiretroviral therapy (cART) in a cohort of naive patients using, for the first time in this context, a path analysis (PA) approach. PATIENTS AND METHODS: Adult patients with chronic infection by subtype B HIV-1 were consecutively enrolled from the start of first-line cART (T0)...
January 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27587695/large-scale-inference-of-conjunctive-bayesian-networks
#18
Hesam Montazeri, Jack Kuipers, Roger Kouyos, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Huldrych F Günthard, Niko Beerenwinkel
UNLABELLED: The continuous time conjunctive Bayesian network (CT-CBN) is a graphical model for analyzing the waiting time process of the accumulation of genetic changes (mutations). CT-CBN models have been successfully used in several biological applications such as HIV drug resistance development and genetic progression of cancer. However, current approaches for parameter estimation and network structure learning of CBNs can only deal with a small number of mutations (<20). Here, we address this limitation by presenting an efficient and accurate approximate inference algorithm using a Monte Carlo expectation-maximization algorithm based on importance sampling...
September 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27587690/patterns-of-amino-acid-conservation-in-human-and-animal-immunodeficiency-viruses
#19
Olga S Voitenko, Andi Dhroso, Anna Feldmann, Dmitry Korkin, Olga V Kalinina
MOTIVATION: Due to their high genomic variability, RNA viruses and retroviruses present a unique opportunity for detailed study of molecular evolution. Lentiviruses, with HIV being a notable example, are one of the best studied viral groups: hundreds of thousands of sequences are available together with experimentally resolved three-dimensional structures for most viral proteins. In this work, we use these data to study specific patterns of evolution of the viral proteins, and their relationship to protein interactions and immunogenicity...
September 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27580334/use-of-flaviviral-genetic-fragments-as-a-potential-prevention-strategy-for-hiv-1-silencing
#20
Muhammad Sheraz, Mazhar Kanak, Mahmudul Hasan, Roshan Bhattarai, Kuhanandha Mahalingam, Leanna A Sealey, Rashshana R Blackwood, Zhabiz Golkar, Ewen McLean, Omar Bagasra
INTRODUCTION: Coinfection with certain members of the Flaviviridae, such as Dengue Virus (DV), West Nile Virus (WNV) Yellow Fever Virus (YFV) and most importantly, GBV-C have been documented to reduce HIV-1 viral load in vivo. Numerous studies strongly support the notion that persistent coinfection with non-pathogenic virus prolongs survival in HIV-1 infected individuals. Coinfected individuals show higher CD4+ cell counts, lower HIV-1 RNA viral loads and live three times longer than clinically matched HIV-1 monoinfected patients...
August 31, 2016: Journal of Infection in Developing Countries
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