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HIV molecular evolution

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https://www.readbyqxmd.com/read/29683851/detection-of-numerous-hiv-1-mo-recombinants-in-france
#1
Fabienne De Oliveira, Pierre Cappy, Véronique Lemée, Alice Moisan, Charlotte Pronier, Laurence Bocket, Magali Bouvier-Alias, Marie-Laure Chaix, Elyanne Gault, Odile Morvan, Jean-Dominique Poveda, Véronique Schneider, Marc Wirden, Elodie Alessandri-Gradt, Thomas Mourez, Jean-Christophe Plantier
BACKGROUND: The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species...
April 19, 2018: AIDS
https://www.readbyqxmd.com/read/29658302/molecular-epidemiology-of-hiv-1-virus-in-puerto-rico-novel-cases-of-hiv-1-subtype-c-d-and-crf-24bg
#2
Pablo Lopez, Omayra De Jesus, Yasuhiro Yamamura, Nayra Rodriguez, Andrea Arias, Raphael Sanchez, Yadira Rodriguez, Vivian Tamayo-Agrait, Wilfredo Cuevas, Vanessa Rivera-Amill
Human immunodeficiency virus-1 (HIV-1) subtype B virus is the most prevalent subtype in Puerto Rico (PR), accounting for about 90% of infection in the island. Recently, other subtypes and circulating recombinant forms (CRF) including F (12_BF), A (01_BF), and CRF-39 BF-like have been identified. The purpose of this study is to assess the distribution of drug resistance mutations and subtypes in PR. A total of 846 nucleotide sequences from the period comprising 2013 through 2017 were obtained from our "HIV Genotyping" test file...
April 15, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29618650/siv-mac239-vif-and-human-apobec3b-interactions-resemble-those-between-hiv-1-vif-and-human-apobec3g
#3
Jiayi Wang, Nadine M Shaban, Allison M Land, William L Brown, Reuben S Harris
Several members of the APOBEC3 DNA cytosine deaminase family can potently inhibit Vif-deficient HIV-1 by catalyzing cytosine deamination in viral cDNA and impeding reverse transcription. HIV-1 counteracts restriction with the virally encoded Vif protein, which targets relevant APOBEC3 proteins for proteasomal degradation. HIV-1 Vif is optimized for degrading the restrictive human APOBEC3 repertoire and, in general, lentiviral Vif proteins specifically target the restricting APOBEC3 enzymes of each host species...
April 4, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29547436/hiv-1-group-p-infection-towards-a-dead-end-infection
#4
Elodie Alessandri-Gradt, Fabienne De Oliveira, Marie Leoz, Véronique Lemee, David L Robertson, Felix Feyertag, Paul-Alain Ngoupo, Philippe Mauclere, François Simon, Jean-Christophe Plantier
OBJECTIVES: HIV/1 group P (HIV-1/P) is the last HIV/1 group discovered and to date, comprises only two strains. To obtain new insights into this divergent group, we screened for new infections by developing specific tools, and analysed phenotypic and genotypic properties of the prototypic strain RBF168. In addition, the follow-up of the unique patient monitored so far, has raised the knowledge of the natural history of this infection and its therapeutic management. DESIGN/METHODS: We developed an HIV-1/P specific sero-molecular strategy and screened over 29,498 specimen samples...
March 15, 2018: AIDS
https://www.readbyqxmd.com/read/29521101/functional-role-of-hsp60-as-a-positive-regulator-of-human-viral-infection-progression
#5
Z Wyżewski, K P Gregorczyk, J Szczepanowska, L Szulc-Dąbrowska
Heat shock proteins (Hsps) are a family of proteins highly conserved in evolution. Members of the Hsp family are mainly responsible for proper protein folding, however they perform many other functions in living organisms. Hsp60 is a molecular chaperone that is present in mitochondria and cytosol of eukaryotic cells, as well as on their surface. It is also found in the extracellular space and in the peripheral blood. Apart from its role in assisting protein folding in cooperation with Hsp10, Hsp60 contributes to regulation of apoptosis, as well as participates in modulation of the immune system activity...
2018: Acta Virologica
https://www.readbyqxmd.com/read/29515569/computational-strategies-for-dissecting-the-high-dimensional-complexity-of-adaptive-immune-repertoires
#6
REVIEW
Enkelejda Miho, Alexander Yermanos, Cédric R Weber, Christoph T Berger, Sai T Reddy, Victor Greiff
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29500940/the-chemical-diversity-and-structure-based-evolution-of-non-peptide-cxcr4-antagonists-with-diverse-therapeutic-potential
#7
REVIEW
Dian Peng, Bin Cao, Ying-Jun Zhou, Ya-Qiu Long
The CXC chemokine receptor 4 (CXCR4) is a highly reserved G-protein coupled 7-transmembrane (TM) chemokine receptor which consists of 352 amino acids. CXCR4 has only one endogenous chemokine ligand of CXCL12, besides several other natural nonchemokine ligands such as extracellular ubiquitin and noncognate ligand of MIF. CXCR4 strongly binds to CXCL12 and the resulting CXCLl2/CXCR4 axis is the molecular basis of their various biological functions, which include: (1) mediating immune and inflammatory response; (2) regulation of hematopoietic stem cell migration and homing; (3) an essential co-receptor for HIV entry into host cells; (4) participation in the process of embryonic development; (5) malignant tumor invasion and metastasis; (6) myocardial infarction, ischemic stroke and acute kidney injury...
February 17, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29492886/workup-of-human-blood-samples-for-deep-sequencing-of-hiv-1-genomes
#8
Marion Cornelissen, Astrid Gall, Antoinette van der Kuyl, Chris Wymant, François Blanquart, Christophe Fraser, Ben Berkhout
We describe a detailed protocol for the manual workup of blood (plasma/serum) samples from individuals infected with the human immunodeficiency virus type 1 (HIV-1) for deep sequence analysis of the viral genome. The study optimizing the assay was performed in the context of the BEEHIVE (Bridging the Evolution and Epidemiology of HIV in Europe) project, which analyzes complete viral genomes from more than 3000 HIV-1-infected Europeans with high-throughput deep sequencing techniques. The goal of the BEEHIVE project is to determine the contribution of viral genetics to virulence...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29473526/there-is-no-difference-between-sequences-of-hiv-1-infected-patients-with-stable-clinical-status-and-hiv-1-reference-sequence
#9
Kazem Baesi, Marzyeh Nili, Katayoun Tayeri, Mohamad Gholami, Samaneh Moallemi, Farzaneh Sabahi, Saber Kalhori, Mehrdad Hasibi
BACKGROUND: The rate of human immunodeficiency virus type 1 (HIV-1) infection in Iran has increased dramatically in the past few years. HIV-1 genome sequences are pivotal for large-scale studies of inter- and intra-host evolution. To understand the molecular difference between reference HIV-1 isolate and two HIV-1 infected patients in Iran, we conducted this study to analyze some genome segments of Iranian HIV-1 isolates. METHODS: Two HIV-1-infected individuals who were under antiretroviral therapy (ARV) for 8 years with stable clinical status were enrolled...
February 21, 2018: Infectious Disorders Drug Targets
https://www.readbyqxmd.com/read/29442996/role-of-framework-mutations-and-antibody-flexibility-in-the-evolution-of-broadly-neutralizing-antibodies
#10
Victor Ovchinnikov, Joy E Louveau, John P Barton, Martin Karplus, Arup K Chakraborty
Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest specific classes of evolutionary lineages: if germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs...
February 14, 2018: ELife
https://www.readbyqxmd.com/read/29431588/aptamers-in-hiv-research-diagnosis-and-therapy
#11
Jyoti Bala, Srinivasan Chinnapaiyan, Rajib Kumar Dutta, Hoshang Unwalla
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range...
February 12, 2018: RNA Biology
https://www.readbyqxmd.com/read/29419684/phylogenetic-and-temporal-dynamics-of-human-immunodeficiency-virus-type-1-crf01_ae-and-crf07_bc-among-recently-infected-antiretroviral-therapy-na%C3%A3-ve-men-who-have-sex-with-men-in-jiangsu-province-china-2012-to-2015-a-molecular-epidemiology-based-study
#12
Yue Yang, Xiu-Ping Zhao, Hua-Chun Zou, Min-Jie Chu, Ping Zhong, Xiao-Shan Li, Xiao-Yan Li, Yu-Hui Yu, Ke-Xin Zhu, Yu-Jia Chen, Fei Xia, Bo-Wen Zhu, Luan-Qi Ruan, Yi-Ning Bao, Xun Zhuang
The prevalence and incidence of human immunodeficiency virus type 1 (HIV-1) among men who have sex with men (MSM) are on the rise throughout China. With a large population of MSM, Jiangsu Province is facing an escalating HIV-1 epidemic.The aim of this study was to explore the phylogenetic and temporal dynamics of HIV-1 CRF01_AE and CRF07_BC among antiretroviral therapy (ART)-naïve MSM recently infected with HIV-1 in Jiangsu Province.We recruited MSM in Jiangsu Province (Suzhou, Wuxi, Nantong, Taizhou and Yancheng) 2012 to 2015...
February 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29403002/effect-of-hiv-hcv-co-infection-on-the-protease-evolution-of-hiv-1b-a-pilot-study-in-a-pediatric-population
#13
Sara Domínguez-Rodríguez, Patricia Rojas, Carolina Fernández McPhee, Israel Pagán, María Luisa Navarro, José Tomás Ramos, África Holguín
This pilot study evaluates in pediatric patients the impact of HIV/HCV coinfection in the molecular evolution of the HIV-1 subtype B protease (HIV-1BPR). For this study, HIV-1B/HCV coinfected (15) and HIV-1B monoinfected (56) patients with available HIV-1B pol sequences were enrolled. Both groups of patients had comparable gender frequencies and average age, time of infection, antiretroviral treatment (ART) exposure and time under ART. Prevalence of drug resistance mutations (DRM), genetic diversity, number of synonymous (dS) and non-synonymous (dN) mutations per site and selection pressures (dN - dS) in the HIV-1BPR were estimated and compared between mono- and coinfected patients...
February 5, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29346413/genetic-diversity-and-potential-routes-of-transmission-of-mycobacterium-bovis-in-mozambique
#14
Adelina Machado, Teresa Rito, Solomon Ghebremichael, Nuelma Muhate, Gabriel Maxhuza, Custodia Macuamule, Ivania Moiane, Baltazar Macucule, Angelica Suzana Marranangumbe, Jorge Baptista, Joaquim Manguele, Tuija Koivula, Elizabeth Maria Streicher, Robin Mark Warren, Gunilla Kallenius, Paul van Helden, Margarida Correia-Neves
Bovine tuberculosis is a zoonotic disease with largely unknown impact in Africa, with risk factors such as HIV and direct contact with animals or consumption of Mycobacterium bovis infected animal products. In order to understand and quantify this risk and design intervention strategies, good epidemiological studies are needed. Such studies can include molecular typing of M. bovis isolates. The aim of this study was to apply these tools to provide novel information concerning the distribution of bovine tuberculosis in cattle in Mozambique and thereby provide relevant information to guide policy development and strategies to contain the disease in livestock, and reduce the risk associated with transmission to humans...
January 2018: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29328787/immune-responses-to-retroviruses
#15
Asier Saez-Cirion, Nicolas Manel
Retroviruses are genome invaders that have shared a long history of coevolution with vertebrates and their immune system. Found endogenously in genomes as traces of past invasions, retroviruses are also considerable threats to human health when they exist as exogenous viruses such as HIV. The immune response to retroviruses is engaged by germline-encoded sensors of innate immunity that recognize viral components and damage induced by the infection. This response develops with the induction of antiviral effectors and launching of the clonal adaptive immune response, which can contribute to protective immunity...
January 12, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29244833/genomic-characterization-and-molecular-evolution-analysis-of-subtype-b-and-bf-recombinant-hiv-1-strains-among-argentinean-men-who-have-sex-with-men-reveal-a-complex-scenario
#16
Cintia G Cevallos, Leandro R Jones, Maria A Pando, Jean K Carr, Maria M Avila, Jorge Quarleri
Currently, data on HIV-1 circulating strains among men who have sex with men (MSM) in Argentina is scarce. In South America, the distribution and the prevalence of BF recombinants are dissimilar and exhibit an underappreciated heterogeneity of recombinant structures. Here, we studied for the first time the genetic diversity of HIV-1 BF recombinants and their evolution over time through in-depth phylogenetic analysis and multiple recombination detection methods involving 337 HIV-1 nucleotide sequences (25 near full-length (NFL) and 312 partial pol gene) obtained from Argentinean MSM...
2017: PloS One
https://www.readbyqxmd.com/read/29228218/nonhuman-primate-models-and-understanding-the-pathogenesis-of-hiv-infection-and-aids
#17
Ronald S Veazey, Andrew A Lackner
Research using nonhuman primates (NHPs) as models for human immunodeficiency virus (HIV) infection and acquired immunodeficiency syndrome (AIDS) has resulted in tremendous achievements not only in the prevention and treatment of HIV, but also in biomedical research more broadly. Once considered a death sentence, HIV infection is now fairly well controlled with combination antiretroviral treatments, almost all of which were first tested for efficacy and safety in nonhuman primates or other laboratory animals...
December 1, 2017: ILAR Journal
https://www.readbyqxmd.com/read/29202081/phylodynamic-applications-in-21-st-century-global-infectious-disease-research
#18
Brittany D Rife, Carla Mavian, Xinguang Chen, Massimo Ciccozzi, Marco Salemi, Jae Min, Mattia Cf Prosperi
Background: Phylodynamics, the study of the interaction between epidemiological and pathogen evolutionary processes within and among populations, was originally defined in the context of rapidly evolving viruses and used to characterize transmission dynamics. The concept of phylodynamics has evolved since the early 21st century, extending its reach to slower-evolving pathogens, including bacteria and fungi, and to the identification of influential factors in disease spread and pathogen population dynamics...
2017: Global Health Research and Policy
https://www.readbyqxmd.com/read/29163435/evolutionary-analysis-of-hiv-1-pol-proteins-reveals-representative-residues-for-viral-subtype-differentiation
#19
Shohei Nagata, Junnosuke Imai, Gakuto Makino, Masaru Tomita, Akio Kanai
RNA viruses have been used as model systems to understand the patterns and processes of molecular evolution because they have high mutation rates and are genetically diverse. Human immunodeficiency virus 1 (HIV-1), the etiological agent of acquired immune deficiency syndrome, is highly genetically diverse, and is classified into several groups and subtypes. However, it has been difficult to use its diverse sequences to establish the overall phylogenetic relationships of different strains or the trends in sequence conservation with the construction of phylogenetic trees...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#20
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas D Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART) and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial and monitored for a median of 107 weeks. Participants started ART with ( n = 9) or without ( n = 9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
February 1, 2018: Journal of Virology
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