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HIV evolution

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https://www.readbyqxmd.com/read/29149197/sieve-analysis-of-breakthrough-hiv-1-sequences-in-hvtn-505-identifies-vaccine-pressure-targeting-the-cd4-binding-site-of-env-gp120
#1
Allan C deCamp, Morgane Rolland, Paul T Edlefsen, Eric Sanders-Buell, Breana Hall, Craig A Magaret, Andrew J Fiore-Gartland, Michal Juraska, Lindsay N Carpp, Shelly T Karuna, Meera Bose, Steven LePore, Shana Miller, Annemarie O'Sullivan, Kultida Poltavee, Hongjun Bai, Kalpana Dommaraju, Hong Zhao, Kim Wong, Lennie Chen, Hasan Ahmed, Derrick Goodman, Matthew Z Tay, Raphael Gottardo, Richard A Koup, Robert Bailer, John R Mascola, Barney S Graham, Mario Roederer, Robert J O'Connell, Nelson L Michael, Merlin L Robb, Elizabeth Adams, Patricia D'Souza, James Kublin, Lawrence Corey, Daniel E Geraghty, Nicole Frahm, Georgia D Tomaras, M Juliana McElrath, Lisa Frenkel, Sheila Styrchak, Sodsai Tovanabutra, Magdalena E Sobieszczyk, Scott M Hammer, Jerome H Kim, James I Mullins, Peter B Gilbert
Although the HVTN 505 DNA/recombinant adenovirus type 5 vector HIV-1 vaccine trial showed no overall efficacy, analysis of breakthrough HIV-1 sequences in participants can help determine whether vaccine-induced immune responses impacted viruses that caused infection. We analyzed 480 HIV-1 genomes sampled from 27 vaccine and 20 placebo recipients and found that intra-host HIV-1 diversity was significantly lower in vaccine recipients (P ≤ 0.04, Q-values ≤ 0.09) in Gag, Pol, Vif and envelope glycoprotein gp120 (Env-gp120)...
2017: PloS One
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#2
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas 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 followed 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...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29140891/the-evolution-of-hiv-testing-continues
#3
Kevin P Delaney, Laura G Wesolowski, Sherry Michele Owen
No abstract text is available yet for this article.
December 2017: Sexually Transmitted Diseases
https://www.readbyqxmd.com/read/29137637/molecular-evolution-of-hiv-1-integrase-during-the-20%C3%A2-years-prior-to-the-first-approval-of-integrase-inhibitors
#4
Karolin Meixenberger, Kaveh Pouran Yousef, Maureen Rebecca Smith, Sybille Somogyi, Stefan Fiedler, Barbara Bartmeyer, Osamah Hamouda, Norbert Bannert, Max von Kleist, Claudia Kücherer
BACKGROUND: Detailed knowledge of the evolutionary potential of polymorphic sites in a viral protein is important for understanding the development of drug resistance in the presence of an inhibitor. We therefore set out to analyse the molecular evolution of the HIV-1 subtype B integrase at the inter-patient level in Germany during a 20-year period prior to the first introduction of integrase strand inhibitors (INSTIs). METHODS: We determined 337 HIV-1 integrase subtype B sequences (amino acids 1-278) from stored plasma samples of antiretroviral treatment-naïve individuals newly diagnosed with HIV-1 between 1986 and 2006...
November 14, 2017: Virology Journal
https://www.readbyqxmd.com/read/29135988/evolution-of-acute-hepatitis-c-virus-infection-in-a-large-european-city-trends-and-new-patterns
#5
César Garriga, Sandra Manzanares-Laya, Patricia García de Olalla, Pilar Gorrindo, Sabela Lens, Ricard Solà, María Martínez-Rebollar, Montserrat Laguno, Jordi Navarro, Xavier Torras, Mercè Gurguí, María-Jesús Barberá, Josep Quer, Eva Masdeu, Pere Simón, Miriam Ros, Anna de Andrés, Joan A Caylà
The aims of this study were to describe the evolution of acute hepatitis C virus (HCV) infections since 2004 and to determine its associated factors. Acute HCV infections diagnosed in Barcelona from 2004 to 2015 were included. Incidence ratios (IR) were then estimated for sex and age groups. Cases were grouped between 2004-2005, 2006-2011 and 2012-2015, and their incidence rate ratios (IRR) were calculated. In addition, risk factors for acute HCV infection were identified using multinomial logistic regression for complete, available and multiple imputed data...
2017: PloS One
https://www.readbyqxmd.com/read/29132792/-neuromeningeal-cryptococcosis-in-patients-infected-with-hiv-at-agadir-regional-hospital-souss-massa-morocco
#6
S Chadli, M Aghrouch, N Taqarort, M Malmoussi, Z Ouagari, F Moustaoui, M Bourouache, S Oulkheir
INTRODUCTION: Neuromeningeal cryptococcosis (NMC) is a severe and fatal opportunistic infection. Lethality is frequent in the absence of treatment, especially in the presence of HIV co-infection. OBJECTIVE: To determine the prevalence, epidemiological, clinical, biological and therapeutic aspects as well as the evolution of NMC for patients infected with HIV. PATIENTS AND METHODS: This is a retrospective study of 40 cases of neuromeningeal cryptococcosis diagnosed in HIV-infected patients...
November 10, 2017: Journal de Mycologie Médicale
https://www.readbyqxmd.com/read/29131825/a-model-based-clustering-method-to-detect-infectious-disease-transmission-outbreaks-from-sequence-variation
#7
Rosemary M McCloskey, Art F Y Poon
Clustering infections by genetic similarity is a popular technique for identifying potential outbreaks of infectious disease, in part because sequences are now routinely collected for clinical management of many infections. A diverse number of nonparametric clustering methods have been developed for this purpose. These methods are generally intuitive, rapid to compute, and readily scale with large data sets. However, we have found that nonparametric clustering methods can be biased towards identifying clusters of diagnosis-where individuals are sampled sooner post-infection-rather than the clusters of rapid transmission that are meant to be potential foci for public health efforts...
November 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29126318/rnase-h-sequence-preferences-influence-antisense-oligonucleotide-efficiency
#8
Lukasz J Kielpinski, Peter H Hagedorn, Morten Lindow, Jeppe Vinther
RNase H cleaves RNA in RNA-DNA duplexes. It is present in all domains of life as well as in multiple viruses and is essential for mammalian development and for human immunodeficiency virus replication. Here, we developed a sequencing-based method to measure the cleavage of thousands of different RNA-DNA duplexes and thereby comprehensively characterized the sequence preferences of HIV-1, human and Escherichia coli RNase H enzymes. We find that the catalytic domains of E. coli and human RNase H have nearly identical sequence preferences, which correlate with the efficiency of RNase H-recruiting antisense oligonucleotides...
November 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29123367/epidemiological-hiv-infection-surveillance-among-subjects-with-risk-behaviours-in-the-city-of-messina-sicily-from-1992-to-2015
#9
REVIEW
G Visalli, E Avventuroso, P Laganà, P Spataro, A Di Pietro, M P Bertuccio, I Picerno
Introduction: Epidemiological studies are a key element in determining the evolution and spread of HIV infection among the world population. Knowledge of the epidemiological dynamics improves strategies for prevention and monitoring. Methods: We examined 2,272 subjects who voluntarily underwent HIV testing from January 1992 to December 2015. For each subject, an anonymous form was completed to obtain information on personal data, sexual habits and exposure to risk factors...
September 2017: Journal of Preventive Medicine and Hygiene
https://www.readbyqxmd.com/read/29122683/high-cxcl10-ip-10-levels-are-a-hallmark-in-the-clinical-evolution-of-the-hiv-infection
#10
Jacqueline María Valverde-Villegas, Rúbia Marília de Medeiros, Joel Henrique Ellwanger, Breno Riegel Santos, Marineide Gonçalves de Melo, Sabrina Esteves de Matos Almeida, José Artur Bogo Chies
The aim of this study was to investigate the modulation of plasma CXCL10, CCL20, CCL22, CCL2, CCL17 and CCL24 levels in HIV-positive patients grouped according to extreme phenotypes of progression to AIDS, and at different stages of HIV infection. HIV-positive individuals with extreme phenotypes of AIDS progression (n=58) at different clinical stages (chronic individuals, both pre-HAART and under-HAART) and HIV-negative controls (n=20) were evaluated. Additionally, HIV-positive individuals that initiated HAART with >350CD4(+)T-cells/mm(3) were compared with those who initiated treatment with <350CD4(+)T-cells/mm(3)...
November 6, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29120736/mind-your-cs-and-gs
#11
Oliver I Fregoso
How can an innate immune sensor shape viral evolution? In recent work, Takata et al. (2017) determined that the antiviral protein ZAP recognizes CG dinucleotide composition to differentiate self from non-self. This pressure may have driven CG dinucleotide suppression in HIV-1 and other RNA viruses to evade host antiviral defenses.
November 8, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/29115368/-evolution-of-the-complexity-index-of-the-antiretroviral-therapy-in-hiv-patients-in-a-real-life-clinical-practice
#12
M Manzano-García, A Robustillo-Cortés, C V Almeida-González, R Morillo-Verdugo
OBJECTIVE: HIV infection has been one of the biggest successes in the healthcare world, mainly due to the appearance of antiretroviral treatment (ART). The complexity of this type of treatment has been one of the decisive factors in the follow-up of these patients. METHODS: An analytical, unicentric, retrospective observational study. We included all patients older than 18 years of age who were diagnosed with HIV who received ART in follow-up for the consultation of pharmaceutical pathology care during the year 2015...
November 7, 2017: Revista Española de Quimioterapia: Publicación Oficial de la Sociedad Española de Quimioterapia
https://www.readbyqxmd.com/read/29091208/cd4-t-cell-decline-following-hiv-seroconversion-in-individuals-with-and-without-cxcr4-tropic-virus
#13
Jade Ghosn, Tatiana Bayan, Karolin Meixenberger, Laurent Tran, Pierre Frange, Antonella d'Arminio Monforte, Robert Zangerle, Carmen de Mendoza, Evguenia Krastinova, Kholoud Porter, Laurence Meyer, Marie-Laure Chaix
Background: The natural clinical and immunological courses following HIV seroconversion with CXCR4-tropic or dual-mixed (X4/DM) viruses are controversial. We compared spontaneous immunological outcome in patients harbouring an X4/DM virus at the time of seroconversion with those harbouring a CCR5-tropic (R5) virus. Methods: Data were included from patients participating in CASCADE, a large cohort collaboration of HIV seroconverters, with ≥2 years of follow-up since seroconversion...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29091198/cd4-cell-count-response-to-first-line-combination-art-in-hiv-2-patients-compared-with-hiv-1-patients-a-multinational-multicohort-european-study
#14
Linda Wittkop, Julie Arsandaux, Ana Trevino, Maarten Schim van der Loeff, Jane Anderson, Ard van Sighem, Jürg Böni, Françoise Brun-Vezinet, Vicente Soriano, Faroudy Boufassa, Norbert Brockmeyer, Alexandra Calmy, François Dabis, Inma Jarrin, Maria Dorrucci, Vitor Duque, Gerd Fätkenheuer, Robert Zangerle, Elena Ferrer, Kholoud Porter, Ali Judd, Nikolaos V Sipsas, Olivier Lambotte, Leah Shepherd, Catherine Leport, Charles Morrison, Cristina Mussini, Niels Obel, Jean Ruelle, Carolyne Schwarze-Zander, Anders Sonnerborg, Ramon Teira, Carlo Torti, Emilia Valadas, Celine Colin, Nina Friis-Møller, Dominique Costagliola, Rodolphe Thiebaut, Geneviève Chene, Sophie Matheron
Background: CD4 cell recovery following first-line combination ART (cART) is poorer in HIV-2+ than in HIV-1+ patients. Only large comparisons may allow adjustments for demographic and pretreatment plasma viral load (pVL). Methods: ART-naive HIV+ adults from two European multicohort collaborations, COHERE (HIV-1 alone) and ACHIeV2e (HIV-2 alone), were included, if they started first-line cART (without NNRTIs or fusion inhibitors) between 1997 and 2011. Patients without at least one CD4 cell count before start of cART, without a pretreatment pVL and with missing a priori-defined covariables were excluded...
October 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29077766/peripheral-blood-hiv-1-dna-dynamics-in-antiretroviral-treated-hiv-hcv-co-infected-patients-receiving-directly-acting-antivirals
#15
Gabriella Rozera, Gabriele Fabbri, Patrizia Lorenzini, Ilaria Mastrorosa, Laura Timelli, Mauro Zaccarelli, Alessandra Amendola, Alessandra Vergori, Maria Maddalena Plazzi, Stefania Cicalini, Andrea Antinori, Maria Rosaria Capobianchi, Isabella Abbate, Adriana Ammassari
BACKGROUND: Aim was to determine the dynamics of peripheral blood mononuclear cells (PBMC)- associated total HIV-1 DNA in successfully ART-treated HIV/HCV co-infected patients receiving DAA treatment and to explore possible virological hypotheses underlying the phenomenon. METHODS: Longitudinal, single-centre study measuring total HIV-1 DNA before the start of DAA, at the end of treatment (EOT), and 3 months after treatment. Univariable and multivariable analyses were used to assess factors associated with HIV-1 DNA increase ≥0...
2017: PloS One
https://www.readbyqxmd.com/read/29065896/harm-reduction-principles-for-healthcare-settings
#16
Mary Hawk, Robert W S Coulter, James E Egan, Stuart Fisk, M Reuel Friedman, Monique Tula, Suzanne Kinsky
BACKGROUND: Harm reduction refers to interventions aimed at reducing the negative effects of health behaviors without necessarily extinguishing the problematic health behaviors completely. The vast majority of the harm reduction literature focuses on the harms of drug use and on specific harm reduction strategies, such as syringe exchange, rather than on the harm reduction philosophy as a whole. Given that a harm reduction approach can address other risk behaviors that often occur alongside drug use and that harm reduction principles have been applied to harms such as sex work, eating disorders, and tobacco use, a natural evolution of the harm reduction philosophy is to extend it to other health risk behaviors and to a broader healthcare audience...
October 24, 2017: Harm Reduction Journal
https://www.readbyqxmd.com/read/29056936/are-evolution-and-the-intracellular-innate-immune-system-key-determinants-in-hiv-transmission
#17
REVIEW
Rebecca P Sumner, Lucy G Thorne, Doug L Fink, Hataf Khan, Richard S Milne, Greg J Towers
HIV-1 is the single most important sexually transmitted disease in humans from a global health perspective. Among human lentiviruses, HIV-1 M group has uniquely achieved pandemic levels of human-to-human transmission. The requirement to transmit between hosts likely provides the strongest selective forces on a virus, as without transmission, there can be no new infections within a host population. Our perspective is that evolution of all of the virus-host interactions, which are inherited and perpetuated from host-to-host, must be consistent with transmission...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29054871/engineering-the-enantioselectivity-and-thermostability-of-a-%C3%AE-lactamase-from-microbacterium-hydrocarbonoxydans-for-the-kinetic-resolution-of-vince-lactam
#18
Shuaihua Gao, Shaozhou Zhu, Rong Huang, Hongxia Li, Hao Wang, Guojun Zheng
To produce promising biocatalysts, natural enzymes often need to be engineered to increase their catalytic performance. In this study, the enantioselectivity and thermostability of a (+)-γ-lactamase from Microbacterium hydrocarbonoxydans as the catalyst in the kinetic resolution of Vince lactam were improved. Enantiomerically pure (-)-Vince lactam is the key synthon in the synthesis of antiviral drugs such as carbovir and abacavir, which are used to fight against human HIV and hepatitis B viruses. The work was initialized by using the combinatorial active-site saturation test strategy to engineer the enantioselectivity of the enzyme...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054249/hiv-1-infected-t-cells-dynamics-and-prognosis-an-evolutionary-game-model
#19
Bahareh Khazaei, Javad Salimi Sartakhti, Mohammad Hossein Manshaei, Quanyan Zhu, Mehdi Sadeghi, Seyed Rasoul Mousavi
BACKGROUND AND OBJECTIVE: Understanding the dynamics of human immunodeficiency virus (HIV) is essential for depicting, developing, and investigating effective treatment strategies. HIV infects several types of immune cells, but its main target is to destroy helper T-cells. In the lymph nodes, the infected T-cells interact with each other and their environment to obtain more resources. According to infectivity and replicative capacity of T-cells in the HIV infection process, they can be divided into four phenotypes...
December 2017: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29046444/relative-resistance-of-mhc-b-to-nef-mediated-downregulation-is-conserved-among-primate-lentiviruses-and-influences-antiviral-t-cell-responses-in-hiv-1-infected-individuals
#20
Francis Mwimanzi, Mako Toyoda, Macdonald Mahiti, Jaclyn K Mann, Jeffrey N Martin, David Bangsberg, Mark A Brockman, Philip Goulder, Frank Kirchhoff, Zabrina L Brumme, Thumbi Ndung'u, Takamasa Ueno
Patient-derived HIV-1 subtype B Nef clones downregulate HLA-A more efficiently than HLA-B. However, it remains unknown whether this property is common to Nef proteins across primate lentiviruses, and how antiviral immune responses may be affected. We examined 263 Nef clones from diverse primate lentiviruses including different pandemic HIV-1 group M subtypes for their ability to downregulate MHC-A and MHC-B from the cell surface. Though lentiviral Nef proteins differed markedly in their absolute MHC-A and MHC-B downregulation abilities, all lentiviral Nef lineages downregulated MHC-A on average 11-32% more efficiently than MHC-B...
October 18, 2017: Journal of Virology
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