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HIV molecular evolution

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https://www.readbyqxmd.com/read/29876136/easy-and-accurate-reconstruction-of-whole-hiv-genomes-from-short-read-sequence-data-with-shiver
#1
Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Nicholas J Croucher, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle Gourlay, M Kate Grabowski, Barbara Gunsenheimer-Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger Kouyos, Oliver Laeyendecker, Kirsi Liitsola, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Marion Cornelissen, Paul Kellam, Peter Reiss, Christophe Fraser
Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29844604/hiv-reverse-transcriptase-and-protease-genes-variability-can-be-a-biomarker-associated-with-hiv-and-hepatitis-b-or-c-coinfection
#2
Natália Mirele Cantão, Lauana Fogaça de Almeida, Ivan Rodrigo Wolf, Rodrigo Oliveira Almeida, Andressa Alves de Almeida Cruz, Caroline Nunes, Alexandre Naime Barbosa, Guilherme Targino Valente, Maria Inês de Moura Campos Pardini, Rejane Maria Tommasini Grotto
Variability of the HIV reverse transcriptase (RT) and protease (PR) genes has been used as indicators of drug resistance and as a mean to evaluate phylogenetic relationships among circulating virus. However, these studies have been carried in HIV mono-infected populations. The goal of this study was to evaluate, for the first time, the HIV PR and RT sequences from HIV/HBV and HIV/HCV co-infected patients. HIV PR and RT genes were amplificated and sequenced to resistance analysis. The bioinformatics analysis was performed to infer about sequences clustering and molecular evolution...
May 29, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29789565/the-wide-utility-of-rabbits-as-models-of-human-diseases
#3
REVIEW
Pedro J Esteves, Joana Abrantes, Hanna-Mari Baldauf, Lbachir BenMohamed, Yuxing Chen, Neil Christensen, Javier González-Gallego, Lorenzo Giacani, Jiafen Hu, Gilla Kaplan, Oliver T Keppler, Katherine L Knight, Xiang-Peng Kong, Dennis K Lanning, Jacques Le Pendu, Ana Lemos de Matos, Jia Liu, Shuying Liu, Ana M Lopes, Shan Lu, Sheila Lukehart, Yukari C Manabe, Fabiana Neves, Grant McFadden, Ruimin Pan, Xuwen Peng, Patricia de Sousa-Pereira, Ana Pinheiro, Masmudur Rahman, Natalie Ruvoën-Clouet, Selvakumar Subbian, Maria Jesús Tuñón, Wessel van der Loo, Michael Vaine, Laura E Via, Shixia Wang, Rose Mage
Studies using the European rabbit Oryctolagus cuniculus contributed to elucidating numerous fundamental aspects of antibody structure and diversification mechanisms and continue to be valuable for the development and testing of therapeutic humanized polyclonal and monoclonal antibodies. Additionally, during the last two decades, the use of the European rabbit as an animal model has been increasingly extended to many human diseases. This review documents the continuing wide utility of the rabbit as a reliable disease model for development of therapeutics and vaccines and studies of the cellular and molecular mechanisms underlying many human diseases...
May 22, 2018: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29765018/tracking-hiv-1-recombination-to-resolve-its-contribution-to-hiv-1-evolution-in-natural-infection
#4
Hongshuo Song, Elena E Giorgi, Vitaly V Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, Bhavna Hora, Peter Hraber, Ethan Romero-Severson, Chunlai Jiang, Xiaojun Li, Shuyi Wang, Hui Li, Jesus F Salazar-Gonzalez, Maria G Salazar, Nilu Goonetilleke, Brandon F Keele, David C Montefiori, Myron S Cohen, George M Shaw, Beatrice H Hahn, Andrew J McMichael, Barton F Haynes, Bette Korber, Tanmoy Bhattacharya, Feng Gao
Recombination in HIV-1 is well documented, but its importance in the low-diversity setting of within-host diversification is less understood. Here we develop a novel computational tool (RAPR (Recombination Analysis PRogram)) to enable a detailed view of in vivo viral recombination during early infection, and we apply it to near-full-length HIV-1 genome sequences from longitudinal samples. Recombinant genomes rapidly replace transmitted/founder (T/F) lineages, with a median half-time of 27 days, increasing the genetic complexity of the viral population...
May 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29758235/innovation-and-trends-in-the-development-and-approval-of-antiviral-medicines-1987-2017-and-beyond
#5
REVIEW
Shuvam Chaudhuri, Julian A Symons, Jerome Deval
2017 marked the 30th anniversary of the approval of zidovudine (AZT) as the first HIV/AIDS therapy. Since then, more than eighty antiviral drugs have received FDA approval, half of which treat HIV infection. Here, we provide a retrospective analysis of approved antiviral drugs, including therapeutics against other major chronic infections such as hepatitis B and C, and herpes viruses, over the last thirty years. During this time, only a few drugs were approved to treat acute viral infections, mainly influenza...
May 15, 2018: Antiviral Research
https://www.readbyqxmd.com/read/29733983/evolutionary-dynamics-of-hepatitis-c-virus-in-a-chronic-hiv-co-infected-patient-and-its-correlation-with-the-immune-status
#6
Andrés Carlos Alberto Culasso, María Cecilia Monzani, Patricia Baré, Rodolfo Hector Campos
The HCV evolutionary dynamics play a key role in the infection onset, maintenance of chronicity, pathogenicity, and drug resistance variants fixation, and are thought to be one of the main caveats in the development of an effective vaccine. Previous studies in HCV/HIV co-infected patients suggest that a decline in the immune status is related with increases in the HCV intra-host genetic diversity. However, these findings are based on single point sequence diversity measures or coalescence analyses in several virus-host interactions...
May 4, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29720497/molecular-mechanisms-for-species-differences-in-organic-anion-transporter-1-oat1-implications-for-renal-drug-toxicity
#7
Ling Zou, Adrian Stecula, Anshul Gupta, Bhagwat Prasad, Huan-Chieh Chien, Sook Wah Yee, Li Wang, Jashvant D Unadkat, Simone H Stahl, Katherine S Fenner, Kathleen M Giacomini
Species differences in renal drug transporters continue to plague drug development with animal models failing to adequately predict renal drug toxicity. For example, adefovir, a renally excreted antiviral drug, failed clinical studies for HIV due to pronounced nephrontoxicity in humans. In this study, we demonstrated that there are large species differences in the kinetics of interactions of a key class of antiviral drugs, acyclic nucleoside phosphonates (ANPs), with OAT1 (SLC22A6) and identified a key amino acid residue responsible for these differences...
May 2, 2018: Molecular Pharmacology
https://www.readbyqxmd.com/read/29683851/detection-of-numerous-hiv-1-mo-recombinants-in-france
#8
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...
June 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
#9
Pablo López, Omayra De Jesús, Yasuhiro Yamamura, Nayra Rodríguez, Andrea Arias, Raphael Sánchez, Yadira Rodríguez, Vivian Tamayo-Agrait, Wilfredo Cuevas, Vanessa Rivera-Amill
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 (CRFs), 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...
May 23, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29618650/simian-immunodeficiency-virus-vif-and-human-apobec3b-interactions-resemble-those-between-hiv-1-vif-and-human-apobec3g
#10
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 human immunodeficiency virus type 1 (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...
June 15, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29547436/hiv-1-group-p-infection-towards-a-dead-end-infection
#11
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
#12
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
#13
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
#14
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...
April 10, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29492886/workup-of-human-blood-samples-for-deep-sequencing-of-hiv-1-genomes
#15
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
#16
Marzyeh Nili, Katayoun Tayeri, Mohamad Gholami, Samaneh Moallemi, Farzaneh Sabahi, Saber Kalhori, Kazem Baesi, 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
#17
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 that there are different classes of evolutionary lineages for the bnAbs...
February 14, 2018: ELife
https://www.readbyqxmd.com/read/29431588/aptamers-in-hiv-research-diagnosis-and-therapy
#18
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...
March 4, 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
#19
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
#20
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
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