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HIV molecular evolution

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https://www.readbyqxmd.com/read/28401776/molecular-characteristics-of-the-envelope-of-vertically-transmitted-hiv-1-strains-from-infants-with-hiv-infection
#1
Manickam Ashokkumar, Manohar Nesakumar, Cheedarla Narayanaiah, Vidya Vijayan Kk, Babu Hemalatha, Srikanth P Tripathy, Luke Elizabeth Hanna
Mother-to-child transmission of HIV offers a good opportunity to study the dynamics of early viral evolution in the host environment to which the virus has partially adapted. Such studies would throw light on the unique features of the infecting viruses, which will subsequently help to design preventive or therapeutic measures against the newly infecting and evolving strains of HIV. Therefore, we undertook a study to determine the genetic divergence of proviral envelope sequences from the HIV infected infants (< 2 years)...
April 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28373274/the-variable-internal-structure-of-the-mycoplasma-penetrans-attachment-organelle-revealed-by-biochemical-and-microscopic-analyses-implications-for-attachment-organelle-mechanism-and-evolution
#2
Steven L Distelhorst, Dominika A Jurkovic, Jian Shi, Grant J Jensen, Mitchell F Balish
Although mycoplasmas have small genomes, many of them, including the HIV-associated opportunist Mycoplasma penetrans, construct a polar attachment organelle (AO) used for both adherence to host cells and gliding motility. However, the irregular phylogenetic distribution of similar structures within the mycoplasmas as well as compositional and ultrastructural differences among these AOs suggest that AOs have arisen several times by convergent evolution. We investigated the ultrastructure and protein composition of the cytoskeleton-like material of the M...
April 3, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28348854/bayesian-codon-substitution-modelling-to-identify-sources-of-pathogen-evolutionary-rate-variation
#3
Guy Baele, Marc A Suchard, Filip Bielejec, Philippe Lemey
Phylodynamic reconstructions rely on a measurable molecular footprint of epidemic processes in pathogen genomes. Identifying the factors that govern the tempo and mode by which these processes leave a footprint in pathogen genomes represents an important goal towards understanding infectious disease evolution. Discriminating between synonymous and non-synonymous substitution rates is crucial for testing hypotheses about the sources of evolutionary rate variation. Here, we implement a codon substitution model in a Bayesian statistical framework to estimate absolute rates of synonymous and non-synonymous substitution in unknown evolutionary histories...
June 2016: Microbial Genomics
https://www.readbyqxmd.com/read/28332348/molecular-epidemiology-of-human-immunodeficiency-virus
#4
REVIEW
Bum Sik Chin
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea...
March 2017: Infection & Chemotherapy
https://www.readbyqxmd.com/read/28187688/identification-of-a-novel-hiv-type-1-recombinant-form-crf01_ae-crf07_bc-in-men-who-have-sex-with-men-in-zhejiang-china
#5
Yufan Xu, Xiaorong Peng, Tiansheng Xie, Xiangyun Lu, Nanping Wu
The prevalence of HIV-1 is increasing rapidly among the population of men who have sex with men (MSM) in China. Here, we report a novel HIV type 1 recombinant form consisting of CRF01_AE and CRF07_BC detected in a male patient through homosexual behavior. A phylogenic analysis revealed that this unique recombinant form (URF) exhibits a complex genomic structure with three CRF07_BC regions inserted into the CRF01_AE backbone. Recently, several second-generation recombinant forms (e.g., CRF01_AE/CRF07_BC) have been identified among MSM in China...
April 12, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28086923/multiple-hiv-1-m%C3%A2-%C3%A2-hiv-1-o-dual-infections-and-new-hiv-1-mo-inter-group-recombinant-forms-detected-in-cameroon
#6
Fabienne De Oliveira, Thomas Mourez, Aurélia Vessiere, Paul-Alain Ngoupo, Elodie Alessandri-Gradt, François Simon, Dominique Rousset, Jean-Christophe Plantier
BACKGROUND: Due to the prevalence of HIV-1 group M and the endemicity of HIV-1 group O infections in Cameroon, patients may be infected with both viruses and/or with HIV-1/MO recombinant forms. Such atypical infections may be deleterious in terms of diagnosis and therapeutic management due to the high divergence of HIV-1/O. The aim of this study was to identify prospectively such atypical infections in Cameroon. RESULTS: Based on serological screening by env-V3 serotyping and a molecular strategy using group-specific (RT)-PCRs, we identified 10 Cameroonian patients harboring three different profiles of infection: (1) 4 HIV-1/M + O dual infections without evidence of recombinant; (2) 5 recombinants associated with one or both parental strains; and (3) 1 new recombinant form without parental strains...
January 13, 2017: Retrovirology
https://www.readbyqxmd.com/read/28005040/-genetic-diversity-of-human-immunodeficiency-viruses-and-antiretroviral-therapy
#7
M R Bobkova
The lecture is devoted to the analysis of the state-of-the-art of the impact of genetic diversity of human immunodeficiency (HIV) viruses on the pattern of infection and the efficiency of antiretroviral therapy (ART). It provides brief information on the origin and evolution of HIV and on the current classification of their genetic variants. The molecular epidemiological situation of HIV infection in Russia and nearby states and the major molecular HIV variants that are dominant in these countries, as well as their origin and prevalence trends are characterized...
2016: Terapevticheskiĭ Arkhiv
https://www.readbyqxmd.com/read/27964762/new-tools-to-analyze-overlapping-coding-regions
#8
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/27906002/hiv-1-genetic-diversity-and-its-distribution-characteristics-among-newly-diagnosed-hiv-1-individuals-in-hebei-province-china
#9
Xinli Lu, Cuiying Zhao, Wei Wang, Chenxi Nie, Yuqi Zhang, Hongru Zhao, Suliang Chen, Ze Cui
BACKGROUND: Since the first HIV-1 case in 1989, Hebei province has presented a clearly rising trend of HIV-1 prevalence, and HIV-1 genetic diversity has become the vital barrier to HIV prevention and control in this area. To obtain detailed information of HIV-1 spread in different populations and in different areas of Hebei, a cross-sectional HIV-1 molecular epidemiological investigation was performed across the province. METHODS: Blood samples of 154 newly diagnosed HIV-1 individuals were collected from ten prefectures in Hebei using stratified sampling...
January 19, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27886568/deep-sequencing-methods-for-protein-engineering-and-design
#10
REVIEW
Emily E Wrenbeck, Matthew S Faber, Timothy A Whitehead
The advent of next-generation sequencing (NGS) has revolutionized protein science, and the development of complementary methods enabling NGS-driven protein engineering have followed. In general, these experiments address the functional consequences of thousands of protein variants in a massively parallel manner using genotype-phenotype linked high-throughput functional screens followed by DNA counting via deep sequencing. We highlight the use of information rich datasets to engineer protein molecular recognition...
November 22, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27867372/overlapping-regions-in-hiv-1-genome-act-as-potential-sites-for-host-virus-interaction
#11
Deeya Saha, Soumita Podder, Tapash C Ghosh
More than a decade, overlapping genes in RNA viruses became a subject of research which has explored various effect of gene overlapping on the evolution and function of viral genomes like genome size compaction. Additionally, overlapping regions (OVRs) are also reported to encode elevated degree of protein intrinsic disorder (PID) in unspliced RNA viruses. With the aim to explore the roles of OVRs in HIV-1 pathogenesis, we have carried out an in-depth analysis on the association of gene overlapping with PID in 35 HIV1- M subtypes...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27798403/a-relaxed-directional-random-walk-model-for-phylogenetic-trait-evolution
#12
Mandev S Gill, Lam Si Tung Ho, Guy Baele, Philippe Lemey, Marc A Suchard
Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes...
May 1, 2017: Systematic Biology
https://www.readbyqxmd.com/read/27733547/positive-selection-of-the-trim-family-regulatory-region-in-primate-genomes
#13
Dan-Dan He, Yueer Lu, Rachel Gittelman, Yabin Jin, Fei Ling, Akey Joshua
Viral selection pressure has acted on restriction factors that play an important role in the innate immune system by inhibiting the replication of viruses during primate evolution. Tripartite motif-containing (TRIM) family members are some of these restriction factors. It is becoming increasingly clear that gene expression differences, rather than protein-coding regions changes, could play a vital role in the anti-retroviral immune mechanism. Increasingly, recent studies have created genome-scale catalogues of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA...
October 12, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27687862/type-specific-detection-of-herpes-simplex-virus-type-1-and-type-2-using-the-cobas%C3%A2-hsv-1-and-2-test-on-the-cobas%C3%A2-4800-platform
#14
Barbara Van Der Pol
HSV-1 and HSV-2 are among the most common causes of sexually transmitted infections (stis) globally. these infections are strongly associated with increased risk of hiv acquisition and rare, but devastating, neonatal disease. available treatment options can reduce HSV transmission and improve quality of life. accurate diagnosis early in disease can improve patient management. Areas covered: This paper describes the clinical manifestations of HSV infection often used for clinical diagnostic purposes. The paper then describes the evolution of laboratory diagnostic assays...
November 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27678053/epistasis-and-pleiotropy-affect-the-modularity-of-the-genotype-phenotype-map-of-cross-resistance-in-hiv-1
#15
Robert Polster, Christos J Petropoulos, Sebastian Bonhoeffer, Frédéric Guillaume
The genotype-phenotype (GP) map is a central concept in evolutionary biology as it describes the mapping of molecular genetic variation onto phenotypic trait variation. Our understanding of that mapping remains partial, especially when trying to link functional clustering of pleiotropic gene effects with patterns of phenotypic trait co-variation. Only on rare occasions have studies been able to fully explore that link and tend to show poor correspondence between modular structures within the GP map and among phenotypes...
December 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/27677159/increasing-prevalence-of-k65k-and-k66k-in-hiv-1-subtype-b-reverse-transcriptase
#16
Sushama Telwatte, Chanson J Brumme, Anna C Hearps, Catherine F Latham, Joshua A Hayward, Secondo Sonza, Nicolas Sluis-Cremer, P Richard Harrigan, Gilda Tachedjian
OBJECTIVE: Synonymous substitutions K65K/K66K in HIV-1 reverse transcriptase alleviate fitness and fidelity defects in HIV-1 molecular clones harboring thymidine analogue mutations (TAMs); however, their potential for transmission and persistence is unknown. Here, we investigated the temporal appearance of K65K/K66K relative to TAMs in a HIV-1 cohort, their prevalence over time, and their impact on viral fitness in the context of patient-derived reverse transcriptase sequences. METHODS: Retrospective analyses of the temporal appearance and longitudinal prevalence of synonymous substitutions and drug resistance mutations were performed using the British Columbia Centre for Excellence in HIV/AIDS Drug Treatment Program (DTP) database...
November 28, 2016: AIDS
https://www.readbyqxmd.com/read/27645997/a-new-class-of-allosteric-hiv-1-integrase-inhibitors-identified-by-crystallographic-fragment-screening-of-the-catalytic-core-domain
#17
Disha Patel, Janet Antwi, Pratibha C Koneru, Erik Serrao, Stefano Forli, Jacques J Kessl, Lei Feng, Nanjie Deng, Ronald M Levy, James R Fuchs, Arthur J Olson, Alan N Engelman, Joseph D Bauman, Mamuka Kvaratskhelia, Eddy Arnold
HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors...
November 4, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27631086/exceptional-heterogeneity-in-viral-evolutionary-dynamics-characterises-chronic-hepatitis-c-virus-infection
#18
Jayna Raghwani, Rebecca Rose, Isabelle Sheridan, Philippe Lemey, Marc A Suchard, Teresa Santantonio, Patrizia Farci, Paul Klenerman, Oliver G Pybus
The treatment of HCV infection has seen significant progress, particularly since the approval of new direct-acting antiviral drugs. However these clinical achievements have been made despite an incomplete understanding of HCV replication and within-host evolution, especially compared with HIV-1. Here, we undertake a comprehensive analysis of HCV within-host evolution during chronic infection by investigating over 4000 viral sequences sampled longitudinally from 15 HCV-infected patients. We compare our HCV results to those from a well-studied HIV-1 cohort, revealing key differences in the evolutionary behaviour of these two chronic-infecting pathogens...
September 2016: PLoS Pathogens
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/27584592/a-chimeric-human-apobec3a-protein-with-a-three-amino-acid-insertion-confers-differential-hiv-1-and-adeno-associated-virus-restriction
#20
Yaqiong Wang, Zekun Wang, Ankita Pramanik, Mario L Santiago, Jianming Qiu, Edward B Stephens
Old World monkey (OWM) and hominid APOBEC3Aproteins exhibit differential restriction activities against lentiviruses and DNA viruses. Human APOBEC3A(hA3A)has weak restriction activity against HIV-1Δvifbut is efficiently restricted by an artificially generated chimeric from mandrills (mndA3A/G). We show that a chimeric hA3Acontaining the "WVS" insertion (hA3A[(27)WVS(29)]) conferred potent HIV-1restriction activity. Analysis of each amino acid of the "WVS" motif show that the length and not necessarily the charge or hydrophobicity of the amino acids accounted for restriction activity...
November 2016: Virology
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