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HIV evolution

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https://www.readbyqxmd.com/read/28935113/directed-evolution-of-glycopeptides-using-mrna-display
#1
Satoru Horiya, Jennifer K Bailey, Isaac J Krauss
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28934209/microbial-translocation-is-correlated-with-hiv-evolution-in-hiv-hcv-co-infected-patients
#2
Jean-Jacques Tudesq, Catherine Dunyach-Remy, Christophe Combescure, Régine Doncesco, Didier Laureillard, Jean-Philippe Lavigne, Albert Sotto
Microbial translocation (MT) is characterized by bacterial products passing into the blood through the gut barrier and is a key phenomenon in the pathophysiology of Human Immunodeficiency Virus (HIV) infection. MT is also associated with liver damage in Hepatitis C Virus (HCV) patients. The aim of the study was to assess MT in plasma of HIV-HCV co-infected patients. 16S rDNA (16 S Ribosomal DNA subunit) marker and other markers of MT such as Lipopolysaccharide (LPS)-binding protein (LBP), soluble CD14 (sCD14), intestinal fatty acid binding protein (I-FABP) were used...
2017: PloS One
https://www.readbyqxmd.com/read/28931681/insights-into-the-impact-of-cd8-immune-modulation-on-hiv-evolutionary-dynamics-in-distinct-anatomical-compartments-using-siv-infected-macaque-models-of-aids-progression
#3
Brittany Rife Magalis, David J Nolan, Patrick Autissier, Tricia H Burdo, Kenneth C Williams, Marco Salemi
A thorough understanding of the role of HIV intra-host evolution in AIDS pathogenesis has been limited by the need for longitudinally sampled viral sequences from the vast target space within the host, which are often difficult to obtain from human subjects. CD8+ lymphocyte-depleted macaques infected with simian immunodeficiency virus (SIV) provide an increasingly utilized model of pathogenesis due to similar clinical manifestations as HIV-1 infection and AIDS progression, as well as characteristic rapid disease onset...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28931679/pathogenic-correlates-of-the-simian-immunodeficiency-virus-siv-associated-b-cell-dysfunction
#4
Egidio Brocca-Cofano, David Kuhrt, Basile Siewe, Cuiling Xu, George S Haret-Richter, Jodi Craigo, Celia Labranche, David C Montefiori, Alan Landay, Cristian Apetrei, Ivona Pandrea
We compared and contrasted pathogenic (pigtailed macaques-PTMs) and nonpathogenic (African green monkeys-AGMs) SIVsab infections to assess the significance of the B-cell dysfunction observed in SIV/HIV infection. We report that the loss of B cells is specifically associated with the pathogenic SIV infection, while in the nonpathogenic natural hosts B cells rapidly increase in both LNs and intestine. SIV-associated B-cell dysfunction associated to the pathogenic SIV infection is characterized by loss of naïve B cells; loss of resting memory B cells due to their redistribution to the gut; increases of the activated B cells and circulating tissue-like memory B cells and expansion of the B regulatory cells...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28928737/env-specific-antibodies-in-chronic-infection-versus-in-vaccination
#5
REVIEW
Martina Soldemo, Gunilla B Karlsson Hedestam
Antibodies are central in vaccine-mediated protection. For HIV-1, a pathogen that displays extreme antigenic variability, B cell responses against conserved determinants of the envelope glycoproteins (Env) are likely required to achieve broadly protective vaccine-induced responses. To understand antibodies in chronic infection, where broad serum neutralizing activity is observed in a subset of individuals, monoclonal antibodies mediating this activity have been isolated. Studies of their maturation pathways reveal that years of co-evolution between the virus and the adaptive immune response are required for such responses to arise...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28918303/decoding-noises-in-hiv-computational-genotyping
#6
MingRui Jia, Timothy Shaw, Xing Zhang, Dong Liu, Ye Shen, Amara E Ezeamama, Chunfu Yang, Ming Zhang
Lack of a consistent and reliable genotyping system can critically impede HIV genomic research on pathogenesis, fitness, virulence, drug resistance, and genomic-based healthcare and treatment. At present, mis-genotyping, i.e., background noises in molecular genotyping, and its impact on epidemic surveillance is unknown. For the first time, we present a comprehensive assessment of HIV genotyping quality. HIV sequence data were retrieved from worldwide published records, and subjected to a systematic genotyping assessment pipeline...
September 14, 2017: Virology
https://www.readbyqxmd.com/read/28918073/a-directed-evolution-approach-to-select-for-novel-adeno-associated-virus-capsids-on-an-hiv-1-producer-t-cell-line
#7
Dawn P Wooley, Priyanka Sharma, John R Weinstein, Poornima Kotha Lakshmi Narayan, David V Schaffer, Katherine J D A Excoffon
A directed evolution approach was used to select for Adeno-associated virus (AAV) capsids that would exhibit more tropism toward an HIV-1 producer T cell line with the long-term goal of developing improved gene transfer vectors. A library of AAV variants was used to infect H9T cells previously infected or uninfected by HIV-1 followed by AAV amplification with wild-type adenovirus. Six rounds of biological selection were performed, including negative selection and diversification after round three. The H9T cells were successfully infected with all three wild-type viruses (AAV, adenovirus, and HIV-1)...
September 13, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28916265/glycans-function-as-anchors-for-antibodies-and-help-drive-hiv-broadly-neutralizing-antibody-development
#8
Raiees Andrabi, Ching-Yao Su, Chi-Hui Liang, Sachin S Shivatare, Bryan Briney, James E Voss, Salar Khan Nawazi, Chung-Yi Wu, Chi-Huey Wong, Dennis R Burton
Apex broadly neutralizing HIV antibodies (bnAbs) recognize glycans and protein surface close to the 3-fold axis of the envelope (Env) trimer and are among the most potent and broad Abs described. The evolution of apex bnAbs from one donor (CAP256) has been studied in detail and many Abs at different stages of maturation have been described. Using diverse engineering tools, we investigated the involvement of glycan recognition in the development of the CAP256.VRC26 Ab lineage. We found that sialic acid-bearing glycans were recognized by germline-encoded and somatically mutated residues on the Ab heavy chain...
September 19, 2017: Immunity
https://www.readbyqxmd.com/read/28912478/the-molecular-epidemiology-of-hiv-1-in-the-comunidad-valenciana-spain-analysis-of-transmission-clusters
#9
Juan Ángel Patiño-Galindo, Manoli Torres-Puente, María Alma Bracho, Ignacio Alastrué, Amparo Juan, David Navarro, María José Galindo, Dolores Ocete, Enrique Ortega, Concepción Gimeno, Josefina Belda, Victoria Domínguez, Rosario Moreno, Fernando González-Candelas
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28906351/prevalence-evolution-and-related-risk-factors-of-kidney-disease-among-spanish-hiv-infected-individuals
#10
Javier Juega-Mariño, Anna Bonjoch, Nuria Pérez-Alvarez, Eugenia Negredo, Beatriu Bayes, Josep Bonet, Buenaventura Clotet, Ramon Romero
Prevalence of kidney disease (KD) is increasing among human immunodeficiency virus (HIV)-infected population. Different factors have been related, varying on different published series.The objectives were to study prevalence of KD in those patients, its evolution, and associated risk factors.An observational cohort study of 1596 HIV-positive patients with cross-sectional data collection in 2008 and 2010 was conducted. We obtained clinical and laboratory markers, and registered previous or current treatment with tenofovir (TDF) and indinavir (IDV)...
September 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28904453/hospital-based-retrospective-study-of-cryptococcal-meningitis-in-a-large-cohort-from-india
#11
Karkal Ravishankar Naik, Aralikatte Onkarappa Saroja, Darshan Kiran Doshi
BACKGROUND: Cryptococcal meningitis is an important and a fatal neuroinfection. Early diagnosis and treatment is of utmost importance in reducing morbidity and mortality. MATERIALS AND METHODS: Data of patients with laboratory-confirmed cryptococcal meningitis seen in tertiary care hospital were reviewed. Details of demographic profile, clinical data, laboratory parameters, complications, and in-hospital mortality were studied. RESULTS: Among 97 patients with cryptococcal meningitis (79 men, 18 women), 88 were HIV-positive, two were diabetic, and seven were sporadic...
July 2017: Annals of Indian Academy of Neurology
https://www.readbyqxmd.com/read/28902679/brief-report-peripheral-monocyte-macrophage-phenotypes-associated-with-the-evolution-of-cognitive-performance-in-hiv-infected-patients
#12
Massimiliano Fabbiani, Antonio Muscatello, Paolo Perseghin, Marco Bani, Arianna Incontri, Nicola Squillace, Giuseppe Lapadula, Andrea Gori, Alessandra Bandera
BACKGROUND: The contribution of monocyte activation in the development of HIV-associated neurocognitive disorders is not completely understood. This study aimed to explore the predictive value of peripheral monocyte/macrophage (M/M) phenotypes on the evolution of cognitive performance in a population of virologically suppressed HIV-infected patients. SETTING: Prospective, observational, longitudinal study. METHODS: HIV-1-infected patients with HIV-RNA <50copies/mL for >12 months underwent neuropsychological examination at baseline and after 1 year...
October 1, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28891813/no-evidence-of-hiv-replication-in-children-on-antiretroviral-therapy
#13
Gert U Van Zyl, Mary Grace Katusiime, Ann Wiegand, William R McManus, Michael J Bale, Elias K Halvas, Brian Luke, Valerie F Boltz, Jonathan Spindler, Barbara Laughton, Susan Engelbrecht, John M Coffin, Mark F Cotton, Wei Shao, John W Mellors, Mary F Kearney
It remains controversial whether current antiretroviral therapy (ART) fully suppresses the cycles of HIV replication and viral evolution in vivo. If replication persists in sanctuary sites such as the lymph nodes, a high priority should be placed on improving ART regimes to target these sites. To investigate the question of ongoing viral replication on current ART regimens, we analyzed HIV populations in longitudinal samples from 10 HIV-1-infected children who initiated ART when viral diversity was low. Eight children started ART at less than ten months of age and showed suppression of plasma viremia for seven to nine years...
September 11, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28879788/development-of-an-epitope-based-hiv-1-vaccine-strategy-from-hiv-1-lipopeptide-to-dendritic-based-vaccines
#14
Mathieu Surenaud, Christine Lacabaratz, Gérard Zurawski, Yves Lévy, Jean-Daniel Lelièvre
Development of a safe, effective and globally affordable Human Immunodeficiency Virus strain 1 (HIV-1) vaccine offers the best hope for future control of the HIV-1 pandemic. However, with the exception of the recent RV144 trial, which elicited a modest level of protection against infection, no vaccine candidate has shown efficacy in preventing HIV-1 infection or in controlling virus replication in humans. There is also a great need for a successful immunotherapeutic vaccine since combination antiretroviral therapy (cART) does not eliminate the reservoir of HIV-infected cells...
September 7, 2017: Expert Review of Vaccines
https://www.readbyqxmd.com/read/28878083/how-germinal-centers-evolve-broadly-neutralizing-antibodies-the-breadth-of-the-follicular-helper-t-cell-response
#15
Rob J De Boer, Alan S Perelson
Many HIV-1 infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years, and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest affinity receptors tend to acquire the most antigen from the FDC network, and present the highest density of cognate peptides to follicular helper T cells (Tfh), which provide survival signals to the B cell. BnAbs are therefore only expected to evolve when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than other lineages of more specific B cells...
September 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28875508/evolution-of-hiv-aids-response-in-brazil-policy-innovations-and-challenges-in-the-fourth-decade-of-the-epidemic
#16
Elize Massard da Fonseca, Francisco Inacio Bastos
Brazil was the first low- and middle-income country to provide universal treatment access to people living with the acquired immunodeficiency syndrome (AIDS), becoming a widely acclaimed model for best practice to managing this epidemic. However, we know little about important challenges to the key pillars of Brazil's response. This article discusses how the evolution of the country's health system institutions and international advancements in AIDS treatment and prevention affected the national response. Decentralization of health system resources and policy making brought fresh challenges to the centralized governance of the national AIDS program and to civil society, weakening their coordination and advocacy capacity...
September 6, 2017: International Journal of Health Planning and Management
https://www.readbyqxmd.com/read/28852587/a-systematic-review-of-differential-rate-of-use-of-the-word-evolve-across-fields
#17
Nina Singh, Matthew T Sit, Marissa K Schutte, Gabriel E Chan, Jeyson E Aldana, Diana Cervantes, Clyde H Himmelstein, Pamela J Yeh
BACKGROUND: Although evolution is the driving force behind many of today's major public health and agriculture issues, both journalists and scientific researchers often do not use the term "evolve" in discussions of these topics. METHODS: In a total of 1,066 articles and 716 papers selected from 25 US newspapers and 34 scientific journals, we assess usage of the word "evolve" and its substitute words in the contexts of cancer tumor drug resistance, HIV drug resistance, mosquito insecticide resistance, and weed pesticide resistance...
2017: PeerJ
https://www.readbyqxmd.com/read/28852572/adaptive-hiv-1-evolutionary-trajectories-are-constrained-by-protein-stability
#18
Abayomi S Olabode, Shaun M Kandathil, Simon C Lovell, David L Robertson
Despite the use of combination antiretroviral drugs for the treatment of HIV-1 infection, the emergence of drug resistance remains a problem. Resistance may be conferred either by a single mutation or a concerted set of mutations. The involvement of multiple mutations can arise due to interactions between sites in the amino acid sequence as a consequence of the need to maintain protein structure. To better understand the nature of such epistatic interactions, we reconstructed the ancestral sequences of HIV-1's Pol protein, and traced the evolutionary trajectories leading to mutations associated with drug resistance...
July 2017: Virus Evolution
https://www.readbyqxmd.com/read/28852479/collapsing-glomerulopathy-a-30-year-perspective-and-single-large-center-experience
#19
L Nicholas Cossey, Christopher P Larsen, Helen Liapis
Collapsing glomerulopathy (CGP) is a pattern of kidney injury seen on renal biopsy with multiple associations and etiologies. It is most commonly described in African-Americans and others with recent African ancestry. The disease is rapidly progressive and often presents with abrupt onset of renal failure and nephrotic-range proteinuria. Since its description 30 years ago, this entity has transformed from a morphologic diagnosis typically seen in the setting of HIV infection to a complicated diagnosis with numerous etiologies, many of which are associated with underlying apolipoprotein L1 (APOL1)-risk variants or other genetic disorders...
August 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28845248/a35%C3%A2-viral-evolution-and-innate-immune-responses-during-acute-hiv-1-infection-and-their-association-with-disease-pathogenesis
#20
A S Hassan, J Hare, G Kamini, L M Yindom, A Kamali, E Karita, W Kilemba, M A Price, P Borrow, P Bjorkman, J Albert, P Kaleebu, S Allan, P Fast, E Hunter, J Gilmour, T Ndung'u, S Rowland-Jones, E J Sanders, J Esbjornsson
No abstract text is available yet for this article.
March 2017: Virus Evolution
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