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HIV bioinformatics

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/27539349/-molecular-epidemiology-and-transmission-of-hiv-in-tianjin-2015
#13
M N Zheng, T L Ning, Y J Gao, X Zhao, L Li, S H Cheng
OBJECTIVE: To understand the characteristics on the diversity of HIV subtypes and related transmission in Tianjin. METHODS: A total of 77 newly diagnosed ART-naïve HIV infectors in 2015 were screened by CD4(+) T cell counts ≥200 cells/μl. Viral RNAs were extracted from plasma samples. Reverse transcription PCR and nested PCR were used to analyze the amplification of pol and env gene fragments, sequencing, and related bioinformatics information. RESULTS: 46...
August 10, 2016: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/27525551/cd4-t-cells-with-an-activated-and-exhausted-phenotype-distinguish-immunodeficiency-during-aviremic-hiv-2-infection
#14
Marcus Buggert, Juliet Frederiksen, Ole Lund, Michael R Betts, Antonio Biague, Morten Nielsen, Johanna Tauriainen, Hans Norrgren, Patrik Medstrand, Annika C Karlsson, Marianne Jansson
OBJECTIVE: HIV type 2 (HIV-2) represents an attenuated form of HIV, in which many infected individuals remain 'aviremic' without antiretroviral therapy. However, aviremic HIV-2 disease progression exists, and in the current study, we therefore aimed to examine if specific pathological characteristics of CD4 T cells are linked to such outcome. DESIGN: HIV-seronegative (n = 25), HIV type 1 (HIV-1) (n = 33), HIV-2 (n = 39, of whom 26 were aviremic), and HIV-1/2 dually (HIV-D) (n = 13)-infected study participants were enrolled from an occupational cohort in Guinea-Bissau...
October 23, 2016: AIDS
https://www.readbyqxmd.com/read/27512062/nf-%C3%AE%C2%BAb-and-irf1-induce-endogenous-retrovirus-k-expression-via-interferon-stimulated-response-elements-in-its-5-long-terminal-repeat
#15
Mamneet Manghera, Jennifer Ferguson-Parry, Rongtuan Lin, Renée N Douville
UNLABELLED: Thousands of endogenous retroviruses (ERV), viral fossils of ancient germ line infections, reside within the human genome. Evidence of ERV activity has been observed widely in both health and disease. While this is most often cited as a bystander effect of cell culture or disease states, it is unclear which signals control ERV transcription. Bioinformatic analysis suggests that the viral promoter of endogenous retrovirus K (ERVK) is responsive to inflammatory transcription factors...
October 15, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27474245/-next-generation-sequencing-for-the-diagnostics-and-epidemiology-of-tuberculosis
#16
Iñaki Comas, Ana Gil
Tuberculosis (TB) has overtaken HIV (human immunodeficiency virus) and malaria as the leading cause of death by an infectious disease worldwide. The reduction in the TB incidence is a modest 2% of cases per year, thus we will need 200 years to eradicate the disease. Part of the problem is that TB control tools are decades old and cannot anymore contribute to accelerate eradication of TB. New diagnostics, treatments and vaccines are urgently needed. Next generation sequencing has the potential to become one of these new tools...
July 2016: Enfermedades Infecciosas y Microbiología Clínica
https://www.readbyqxmd.com/read/27459300/expression-of-a-recombinant-anti-hiv-and-anti-tumor-protein-map30-in-nicotiana-tobacum-hairy-roots-a-ph-stable-and-thermophilic-antimicrobial-protein
#17
Ali Moghadam, Ali Niazi, Alireza Afsharifar, Seyed Mohsen Taghavi
In contrast to conventional antibiotics, which microorganisms can readily evade, it is nearly impossible for a microbial strain that is sensitive to antimicrobial proteins to convert to a resistant strain. Therefore, antimicrobial proteins and peptides that are promising alternative candidates for the control of bacterial infections are under investigation. The MAP30 protein of Momordica charantia is a valuable type I ribosome-inactivating protein (RIP) with anti-HIV and anti-tumor activities. Whereas the antimicrobial activity of some type I RIPs has been confirmed, less attention has been paid to the antimicrobial activity of MAP30 produced in a stable, easily handled, and extremely cost-effective protein-expression system...
2016: PloS One
https://www.readbyqxmd.com/read/27453827/emerging-role-of-bioinformatics-tools-and-software-in-evolution-of-clinical-research
#18
REVIEW
Supreet Kaur Gill, Ajay Francis Christopher, Vikas Gupta, Parveen Bansal
Clinical research is making toiling efforts for promotion and wellbeing of the health status of the people. There is a rapid increase in number and severity of diseases like cancer, hepatitis, HIV etc, resulting in high morbidity and mortality. Clinical research involves drug discovery and development whereas clinical trials are performed to establish safety and efficacy of drugs. Drug discovery is a long process starting with the target identification, validation and lead optimization. This is followed by the preclinical trials, intensive clinical trials and eventually post marketing vigilance for drug safety...
July 2016: Perspectives in Clinical Research
https://www.readbyqxmd.com/read/27448822/multiplexed-next-generation-sequencing-and-de-novo-assembly-to-obtain-near-full-length-hiv-1-genome-from-plasma-virus
#19
Shambhu G Aralaguppe, Abu Bakar Siddik, Ashokkumar Manickam, Anoop T Ambikan, Milner M Kumar, Sunjay Jude Fernandes, Wondwossen Amogne, Dhinoth K Bangaruswamy, Luke Elizabeth Hanna, Anders Sonnerborg, Ujjwal Neogi
Analysing the HIV-1 near full-length genome (HIV-NFLG) facilitates new understanding into the diversity of virus population dynamics at individual or population level. In this study we developed a simple but high-throughput next generation sequencing (NGS) protocol for HIV-NFLG using clinical specimens and validated the method against an external quality control (EQC) panel. Clinical specimens (n=105) were obtained from three cohorts from two highly conserved HIV-1C epidemics (India and Ethiopia) and one diverse epidemic (Sweden)...
October 2016: Journal of Virological Methods
https://www.readbyqxmd.com/read/27440900/hiv-1-vpr-inhibits-kaposi-s-sarcoma-associated-herpesvirus-lytic-replication-by-inducing-microrna-mir-942-5p-and-activating-nf-%C3%AE%C2%BAb-signaling
#20
Qin Yan, Chenyou Shen, Jie Qin, Wan Li, Minmin Hu, Hongmei Lu, Di Qin, Jianzhong Zhu, Shou-Jiang Gao, Chun Lu
UNLABELLED: Kaposi's sarcoma-associated herpesvirus (KSHV) infection is required for the development of several AIDS-related malignancies, including Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL). The high incidence of AIDS-KS has been ascribed to the interaction of KSHV and HIV-1. We have previously shown that HIV-1-secreted proteins Tat and Nef regulate the KSHV life cycle and synergize with KSHV oncogenes to promote angiogenesis and tumorigenesis. Here, we examined the regulation of KSHV latency by HIV-1 viral protein R (Vpr)...
October 1, 2016: Journal of Virology
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