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https://www.readbyqxmd.com/read/27928014/histidine-375-modulates-cd4-binding-in-hiv-1-crf01_ae-envelope-glycoproteins
#1
Daria Zoubchenok, Maxime Veillette, Jérémie Prévost, Eric Sanders-Buell, Kshitij Wagh, Bette Korber, Agnès L Chenine, Andrés Finzi
: The envelope glycoproteins (Env) from human immunodeficiency virus type 1 (HIV-1) mediate viral entry. The binding of the HIV-1 gp120 glycoprotein to CD4 triggers conformational changes in gp120 that allow high-affinity binding to its coreceptors. Contrary to all other Envs from the same phylogenetic group M, which possess a serine (S) at position 375, those from CRF01_AE strains possess a histidine (H) at this location. This residue is part of the Phe43 cavity where residue 43 of CD4 (a phenylalanine) engages with the gp120...
December 7, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27923769/recombination-in-hepatitis-c-virus-is-not-uncommon-among-people-who-inject-drugs-in-kolkata-india
#2
Debanjali Gupta, Kallol Saha, Aritra Biswas, Rushna Firdaus, Monika Ghosh, Provash Chandra Sadhukhan
Recombination in RNA virus is a rare event in the survival and evolution to evade host immune system. This is increasing within high risk group population (HRG) due to super infection that occurs by continuous sharing of common drug equipment by HCV infected or HIV-HCV co-infected recurrent drug users. Recombination causes impediment to vaccine development and therapeutic intervention as standard HCV treatment is still genotype specific. Blood samples of 194 people who inject drugs (PWID) were collected from an Opioid Substitution Therapy Centre in Kolkata,India...
December 3, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27916968/ion-channel-activity-of-vpu-proteins-is-conserved-throughout-evolution-of-hiv-1-and-siv
#3
Timo Greiner, Sebastian Bolduan, Brigitte Hertel, Christine Groß, Kay Hamacher, Ulrich Schubert, Anna Moroni, Gerhard Thiel
The human immunodeficiency virus type 1 (HIV-1) protein Vpu is encoded exclusively by HIV-1 and related simian immunodeficiency viruses (SIVs). The transmembrane domain of the protein has dual functions: it counteracts the human restriction factor tetherin and forms a cation channel. Since these two functions are causally unrelated it remains unclear whether the channel activity has any relevance for viral release and replication. Here we examine structure and function correlates of different Vpu homologs from HIV-1 and SIV to understand if ion channel activity is an evolutionary conserved property of Vpu proteins...
December 1, 2016: Viruses
https://www.readbyqxmd.com/read/27912737/hcv-prevalence-can-predict-hiv-epidemic-potential-among-people-who-inject-drugs-mathematical-modeling-analysis
#4
Vajiheh Akbarzadeh, Ghina R Mumtaz, Susanne F Awad, Helen A Weiss, Laith J Abu-Raddad
BACKGROUND: Hepatitis C virus (HCV) and HIV are both transmitted through percutaneous exposures among people who inject drugs (PWID). Ecological analyses on global epidemiological data have identified a positive association between HCV and HIV prevalence among PWID. Our objective was to demonstrate how HCV prevalence can be used to predict HIV epidemic potential among PWID. METHODS: Two population-level models were constructed to simulate the evolution of HCV and HIV epidemics among PWID...
December 3, 2016: BMC Public Health
https://www.readbyqxmd.com/read/27907076/clinical-determinants-of-hiv-1b-between-host-evolution-and-their-association-with-drug-resistance-in-pediatric-patients
#5
Israel Pagán, Patricia Rojas, José Tomás Ramos, África Holguín
Understanding the factors that modulate the evolution of virus populations is essential to design efficient control strategies. Mathematical models predict that factors affecting viral within-host evolution may also determine that at the between-host level. Although HIV-1 within-host evolution has been associated with clinical factors used to monitor AIDS progression, such as patient age, CD4 cells count, viral load, and antiretroviral experience, little is known about the role of these clinical factors in determining between-host HIV-1 evolution...
2016: PloS One
https://www.readbyqxmd.com/read/27906002/hiv-1-genetic-diversity-and-its-distribution-characteristics-among-newly-diagnosed-hiv-1-individuals-in-hebei-province-china
#6
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/27906001/evolution-of-changes-in-cognitive-function-after-the-initiation-of-antiretroviral-therapy
#7
Borja Mora-Peris, Elizabeth Stevens, Francesca Ferretti, Jonathan Underwood, Stephen Taylor, Alan Winston
BACKGROUND: Cognitive function is reported to improve after the initiation of combination antiretroviral therapy (cART). Data on the evolution of such changes are limited. We assessed the dynamics of changes in cognitive parameters, in HIV-positive subjects initiating cART. METHODS: Cognitive function in seven domains was evaluated for HIV-infected patients without clinically significant cognitive impairment prior to the initiation of cART, and 24 and 48 weeks after...
April 14, 2016: AIDS Research and Therapy
https://www.readbyqxmd.com/read/27903602/whole-genome-sequencing-of-mycobacterium-tuberculosis-provides-insight-into-the-evolution-and-genetic-composition-of-drug-resistant-tuberculosis-in-belarus
#8
Kurt R Wollenberg, Christopher A Desjardins, Aksana Zalutskaya, Vervara Slodovnikova, Andrew J Oler, Mariam Quiñones, Thomas Abeel, Sinead B Chapman, Michael Tartakovsky, Andrei Gabrielian, Sven Hoffner, Aliaksandr Skrahin, Bruce W Birren, Alexander Rosenthal, Alena Skrahina, Ashlee M Earl
The emergence and spread of drug resistant Mycobacterium tuberculosis (DR-TB) is a critical global health issue. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB...
November 30, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27899706/mixed-hidden-markov-quantile-regression-models-for-longitudinal-data-with-possibly-incomplete-sequences
#9
Maria Francesca Marino, Nikos Tzavidis, Marco Alfò
Quantile regression provides a detailed and robust picture of the distribution of a response variable, conditional on a set of observed covariates. Recently, it has be been extended to the analysis of longitudinal continuous outcomes using either time-constant or time-varying random parameters. However, in real-life data, we frequently observe both temporal shocks in the overall trend and individual-specific heterogeneity in model parameters. A benchmark dataset on HIV progression gives a clear example. Here, the evolution of the CD4 log counts exhibits both sudden temporal changes in the overall trend and heterogeneity in the effect of the time since seroconversion on the response dynamics...
November 28, 2016: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/27898525/characterization-of-hcv-ns3-protease-variants-in-hcv-hiv-coinfected-patients-by-ultra-deep-sequence-analysis-relationship-to-hepatic-fibrosis
#10
Enass A Abdel-Hameed, Susan D Rouster, Xiang Zhang, Jing Chen, Mario Medvedovic, Zachary D Goodman, Kenneth E Sherman
BACKGROUND: Treatment of HCV/HIV coinfection is now largely based upon utilization of direct acting agents. Pre-treatment viral resistant-associated variants (RAVs) and host liver condition may affect the sustained virological response. In this study, we explored relative prevalence of protease resistance-associated mutations, the evolution of those RAVs following 12 weeks of pegylated interferon alfa exposure, and the role hepatic fibrosis might have on RAV display. METHODS: Thirty nonresponder HCV/ HIV coinfected subjects were evaluated pre- and post- 12 weeks of pegIFN treatment...
November 25, 2016: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/27888126/understanding-the-complex-evolution-of-rapidly-mutating-viruses-with-deep-sequencing-beyond-the-analysis-of-viral-diversity
#11
REVIEW
Preston Leung, Auda A Eltahla, Andrew R Lloyd, Rowena A Bull, Fabio Luciani
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts...
November 22, 2016: Virus Research
https://www.readbyqxmd.com/read/27886568/deep-sequencing-methods-for-protein-engineering-and-design
#12
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/27881614/performance-characteristics-of-a-new-consensus-commercial-kit-for-hepatitis-d-virus-rna-viral-load-quantification
#13
Frédéric Le Gal, Samira Dziri, Athenaïs Gerber, Chakib Alloui, Zahia Ben Abdesselam, Dominique Roulot, Ségolène Brichler, Emmanuel Gordien
Hepatitis Delta virus (HDV) is responsible for fulminant hepatitis and liver failure, and accelerates evolution towards cirrhosis and hepatocellular carcinoma in hepatitis B virus-infected patients. To date treatment relies upon long-term administration of pegylated alpha-interferon with sustained virological response in 30% of the patients. Very recently, new promising anti HDV therapies have been developed and are already used in clinical trials. HDV-RNA viral load (HDVL) monitoring must be an integral part of the management of the infected-patients...
November 23, 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27875372/cutaneous-malignancies-in-hiv
#14
Aileen Y Chang, Phil Doiron, Toby Maurer
PURPOSE OF REVIEW: As patients with HIV infection are living longer with their disease, we have seen the evolution of skin cancer in this population. Cancer registries have not documented the incidence and prevalence of these cancers but we do have relevant data from cohorts. This article attempts to bring to light the extent to which skin cancer is an issue in HIV disease both domestically and internationally. RECENT FINDINGS: Squamous cell cancer is increasing in incidence in the United States and elsewhere...
January 2017: Current Opinion in HIV and AIDS
https://www.readbyqxmd.com/read/27867372/overlapping-regions-in-hiv-1-genome-act-as-potential-sites-for-host-virus-interaction
#15
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/27856703/hiv-1-drug-resistance-mutations-emerging-on-darunavir-therapy-in-pi-naive-and-experienced-patients-in-the-uk
#16
Kate El Bouzidi, Ellen White, Jean L Mbisa, Caroline A Sabin, Andrew N Phillips, Nicola Mackie, Anton L Pozniak, Anna Tostevin, Deenan Pillay, David T Dunn
BACKGROUND: Darunavir is considered to have a high genetic barrier to resistance. Most darunavir-associated drug resistance mutations (DRMs) have been identified through correlation of baseline genotype with virological response in clinical trials. However, there is little information on DRMs that are directly selected by darunavir in clinical settings. OBJECTIVES: We examined darunavir DRMs emerging in clinical practice in the UK. PATIENTS AND METHODS: Baseline and post-exposure protease genotypes were compared for individuals in the UK Collaborative HIV Cohort Study who had received darunavir; analyses were stratified for PI history...
December 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27855060/establishment-and-stability-of-the-latent-hiv-1-dna-reservoir
#17
Johanna Brodin, Fabio Zanini, Lina Thebo, Christa Lanz, Göran Bratt, Richard A Neher, Jan Albert
HIV-1 infection cannot be cured because the virus persists as integrated proviral DNA in long-lived cells despite years of suppressive antiretroviral therapy (ART). In a previous paper (Zanini, 2015) we documented HIV-1 evolution 10 untreated patients. Here we characterize establishment, turnover, and evolution of viral DNA reservoirs in the same patients after 3-18 years of suppressive ART. A median of 14\% (range 0-42\%) of the DNA sequences were defective due to G-to-A hypermutation. Remaining DNA sequences showed no evidence of evolution over years of suppressive ART...
November 15, 2016: ELife
https://www.readbyqxmd.com/read/27851829/diversification-in-the-hiv-1-envelope-hyper-variable-domains-v2-v4-and-v5-and-higher-probability-of-transmitted-founder-envelope-glycosylation-favor-the-development-of-heterologous-neutralization-breadth
#18
S Abigail Smith, Samantha L Burton, William Kilembe, Shabir Lakhi, Etienne Karita, Matt Price, Susan Allen, Eric Hunter, Cynthia A Derdeyn
A recent study of plasma neutralization breadth in HIV-1 infected individuals at nine International AIDS Vaccine Initiative (IAVI) sites reported that viral load, HLA-A*03 genotype, and subtype C infection were strongly associated with the development of neutralization breadth. Here, we refine the findings of that study by analyzing the impact of the transmitted/founder (T/F) envelope (Env), early Env diversification, and autologous neutralization on the development of plasma neutralization breadth in 21 participants identified during recent infection at two of those sites: Kigali, Rwanda (n = 9) and Lusaka, Zambia (n = 12)...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27821148/understanding-pneumococcal-serotype-1-biology-through-population-genomic-analysis
#19
Chrispin Chaguza, Jennifer E Cornick, Simon R Harris, Cheryl P Andam, Laura Bricio-Moreno, Marie Yang, Feyruz Yalcin, Sani Ousmane, Shanil Govindpersad, Madikay Senghore, Chinelo Ebruke, Mignon Du Plessis, Anmol M Kiran, Gerd Pluschke, Betuel Sigauque, Lesley McGee, Keith P Klugman, Paul Turner, Jukka Corander, Julian Parkhill, Jean-Marc Collard, Martin Antonio, Anne von Gottberg, Robert S Heyderman, Neil French, Aras Kadioglu, William P Hanage, Dean B Everett, Stephen D Bentley
BACKGROUND: Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. METHODS: We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries...
November 8, 2016: BMC Infectious Diseases
https://www.readbyqxmd.com/read/27815125/meeting-report-29th-international-conference-on-antiviral-research-in-la-jolla-ca-usa
#20
REVIEW
R Anthony Vere Hodge
The 29th International Conference on Antiviral Research (ICAR) was held in La Jolla, CA, USA from April 17 to 21, 2016. This report opens with a tribute to the late Chris McGuigan, a Past-President of ISAR, then continues with summaries of the principal invited lectures. Doug Richman (Elion Award) investigated HIV resistance, Bob Vince (Holý Award) showed how carbocyclic nucleoside analogs led to abacavir and Jerome Deval (Prusoff Award) explained how his group chose to seek a nucleoside analog to treat RSV...
November 1, 2016: Antiviral Research
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