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HIV evolution

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https://www.readbyqxmd.com/read/28645318/detecting-consistent-patterns-of-directional-adaptation-using-differential-selection-codon-models
#1
Sahar Parto, Nicolas Lartillot
BACKGROUND: Phylogenetic codon models are often used to characterize the selective regimes acting on protein-coding sequences. Recent methodological developments have led to models explicitly accounting for the interplay between mutation and selection, by modeling the amino acid fitness landscape along the sequence. However, thus far, most of these models have assumed that the fitness landscape is constant over time. Fluctuations of the fitness landscape may often be random or depend on complex and unknown factors...
June 23, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28639993/peripheral-monocytes-macrophages-phenotypes-associated-to-the-evolution-of-cognitive-performance-in-hiv-infected-patients
#2
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 one year...
June 19, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28628526/determinants-of-hiv-1-cd4-independent-brain-adaptation
#3
Madina Shakirzyanova, Xiang-Peng Kong, Cecilia Cheng-Mayer
BACKGROUND: HIV-1 is known to adapt to the local environment in its usage of receptors and it can become CD4 independent in the brain where the receptor is scarce. This adaptation is through amino acid variations, but the patterns of such variation are not yet well understood. Given that infection of long-lived CD4-low and CD4-negative cells in anatomic compartments such as the brain expand cell tropism in vivo and may serve as potential viral reservoirs that pose challenge for HIV eradication, understanding the evolution to CD4-independence and envelope conformation associated with infection in the absence of CD4 will not only broaden our insights into HIV pathogenesis, but may guide functional cure strategies as well...
June 15, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/28623276/gag-protease-coevolution-analyses-define-novel-structural-surfaces-in-the-hiv-1-matrix-and-capsid-involved-in-resistance-to-protease-inhibitors
#4
Francisco M Codoñer, Ruth Peña, Oscar Blanch-Lombarte, Esther Jimenez-Moyano, Maria Pino, Thomas Vollbrecht, Bonaventura Clotet, Javier Martinez-Picado, Rika Draenert, Julia G Prado
Despite the major role of Gag in establishing resistance of HIV-1 to protease inhibitors (PIs), very limited data are available on the total contribution of Gag residues to resistance to PIs. To identify in detail Gag residues and structural interfaces associated with the development of HIV-1 resistance to PIs, we traced viral evolution under the pressure of PIs using Gag-protease single genome sequencing and coevolution analysis of protein sequences in 4 patients treated with PIs over a 9-year period. We identified a total of 38 Gag residues correlated with the protease, 32 of which were outside Gag cleavage sites...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28604782/viral-genetic-variation-accounts-for-a-third-of-variability-in-hiv-1-set-point-viral-load-in-europe
#5
François Blanquart, Chris Wymant, Marion Cornelissen, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle J 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, Guido Vanham, Ben Berkhout, Paul Kellam, Peter Reiss, Christophe Fraser
HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evolution of the viral population, we must quantify the heritability of set-point viral load, which is the fraction of variation in this phenotype attributable to viral genetic variation. However, current estimates of heritability vary widely, from 6% to 59%. Here we used a dataset of 2,028 seroconverters infected between 1985 and 2013 from 5 European countries (Belgium, Switzerland, France, the Netherlands and the United Kingdom) and estimated the heritability of set-point viral load at 31% (CI 15%-43%)...
June 2017: PLoS Biology
https://www.readbyqxmd.com/read/28592539/hiv-1-epitope-variability-is-associated-with-t-cell-receptor-repertoire-instability-and-breadth
#6
Arumugam Balamurugan, Deon Claiborne, Hwee L Ng, Otto O Yang
Mutational escape of HIV-1 from HIV-1-specific CD8(+) T lymphocytes (CTLs) is a major barrier for effective immune control. Each epitope typically is targeted by multiple clones with distinct T cell receptors (TCRs). While the clonal repertoire may be important for containing epitope variation, determinants of its composition are poorly understood. We investigate the clonal repertoire of 29 CTL responses against 23 HIV-1 epitopes longitudinally in nine chronically infected untreated subjects with plasma viremia <3000 RNA copies/ml over 17 to 179 weeks...
June 7, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28586237/a-unique-second-generation-recombinant-form-of-hiv-1-identified-among-men-who-have-sex-with-men%C3%AF-msm%C3%AF-in-beijing-china
#7
Xue Li, Mingqiang Hao, Yinxiao Hao, Jingrong Ye, Ruolei Xin, Hongyan Lu
In China, CRF01_AE and CRF07_BC are the most circulating strains of HIV-1, more and more second-generation recombinant forms have been isolated around the two strains. The same situation happened in Beijing recent years. In our finding, we have isolated a new second-generation recombinant form of HIV-1 from one male patient who infected by homosexual behavior. Polygenetic analysis revealed that the sequence includes five CRF01-AE fragments and four CRF07_BC fragments. CRF01_AE as this recombinant's skeleton and four CRF07_BC fragments inserted into it...
June 6, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28584718/the-increasing-prevalence-of-hiv-helicobacter-pylori-co-infection-over-time-along-with-the-evolution-of-antiretroviral-therapy-art
#8
Aleksandra Radovanović Spurnić, Branko Brmbolić, Zorica Stojšić, Tatijana Pekmezović, Zoran Bukumirić, Miloš Korać, Dubravka Salemović, Ivana Pešić-Pavlović, Goran Stevanović, Ivana Milošević, Djordje Jevtović
Helicobacter pylori (H. pylori) is one of the most common human bacterial infections with prevalence rates between 10-80% depending upon geographical location, age and socioeconomic status. H. pylori is commonly found in patients complaining of dyspepsia and is a common cause of gastritis. During the course of their infection, people living with HIV (PLHIV) often have a variety of gastrointestinal symptoms including dyspepsia and while previous studies have reported HIV and H. pylori co-infection, there has been little data clarifying the factors influencing this...
2017: PeerJ
https://www.readbyqxmd.com/read/28582393/high-correlation-between-framingham-equations-with-bmi-and-with-lipids-to-estimate-cardiovascular-risks-score-at-baseline-in-hiv-infected-adults-in-the-temprano-trial-anrs-12136-in-c%C3%A3-te-d-ivoire
#9
Calixte Ghehi, Delphine Gabillard, Raoul Moh, Anani Badje, Gérard Menan Kouamé, Eric Oouttara, Hugues Ahibo, Jean Baptiste N'Takpé, Jérôme Lecarrou, Serge Paul Eholié, Xavier Anglaret, Christine Danel
CONTEXT: Data on cardiovascular risk (CVR) score among HIV-infected patients in sub-Saharan Africa are scarce. Our first objective was to compare the CVR score of Framingham utilizing BMI and lipids at baseline, and secondary to assess evolution of CVR score over time at Month 30 in the Temprano trial. METHODS: HIV-infected adults with CD4 <800/mm3 without criteria for initiating ART were included and followed for 30 months in the Temprano trial, which assessed the benefits and risks of early antiretroviral treatment (ART) vs deferred ART...
2017: PloS One
https://www.readbyqxmd.com/read/28571570/immunological-and-virological-characterization-of-hiv-1-viremia-controllers-in-the-north-region-of-brazil
#10
Samara Tatielle M Gomes, Érica R Gomes, Mike B Dos Santos, Sandra S Lima, Maria Alice F Queiroz, Luiz Fernando A Machado, Izaura M V Cayres-Vallinoto, Antonio Carlos R Vallinoto, Marluísa de O Guimarães Ishak, Ricardo Ishak
BACKGROUND: A rare phenotype of clinical non-progressors to AIDS is not well understood and the new protocol for universal treatment, may block the understanding of viral control thus it is crucial to define this controversial group. METHODS: A cohort of 30 persons followed a criteria for viremia control groups 1 (VC1; n = 2) and 2 (VC2; n = 7) and non-viral controllers (NC; n = 21) including number of years of diagnosis, LTCD4(+), LTCD8(+) counts, plasma viral load and the absence of ART; 241 uninfected control persons were matched to age and sex...
June 1, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28561925/evolution-of-sensory-neuropathy-after-initiation-of-antiretroviral-therapy
#11
Chad M Centner, Francesca Little, Johan J van der Watt, John-Randel Vermaak, Joel A Dave, Naomi S Levitt, Jeannine M Heckmann
INTRODUCTION: We studied the evolution of sensory neuropathy after antiretroviral therapy (ART) in HIV-infected South Africans. METHODS: Enrolment commenced before ART with 6-monthly follow-up for 24 months. Symptomatic distal sensory polyneuropathy (SDSP) was defined as one symptom and sign. Symptom/sign scores were compared between visits. RESULTS: We enrolled 184 participants. Pre-ART, 16% had SDSP. After 18 months of ART, pain prevalence decreased in those with pre-ART SDSP (odds ratio [OR] 0...
May 31, 2017: Muscle & Nerve
https://www.readbyqxmd.com/read/28551370/multiple-introductions-and-onward-transmission-of-hiv-1-subtype-b-strains-in-shanghai-china
#12
Xiaoshan Li, Kexin Zhu, Yile Xue, Feiran Wei, Rong Gao, Ralf Duerr, Kun Fang, Wei Li, Yue Song, Guoping Du, Wenjuan Yan, Taha Hussein Musa, You Ge, Yu Ji, Ping Zhong, Pingmin Wei
OBJECTIVE: To investigate the viral genetic evolution, spatial origins and patterns of transmission of HIV-1 subtype B in Shanghai, China. METHODS: A total of 242 Shanghai subtype B and 1519 reference pol sequences were subjected to phylogenetic inference and genetic transmission network analyses. RESULTS: Phylogenetic analyses revealed that subtype B strains circulating in Shanghai were genetically diverse and closely associated with viral sequence lineages in Beijing (76 of 242 [31...
May 24, 2017: Journal of Infection
https://www.readbyqxmd.com/read/28542584/the-emergence-and-evolution-of-the-research-fronts-in-hiv-aids-research
#13
David Fajardo-Ortiz, Malaquias Lopez-Cervantes, Luis Duran, Michel Dumontier, Miguel Lara, Hector Ochoa, Victor M Castano
In this paper, we have identified and analyzed the emergence, structure and dynamics of the paradigmatic research fronts that established the fundamentals of the biomedical knowledge on HIV/AIDS. A search of papers with the identifiers "HIV/AIDS", "Human Immunodeficiency Virus", "HIV-1" and "Acquired Immunodeficiency Syndrome" in the Web of Science (Thomson Reuters), was carried out. A citation network of those papers was constructed. Then, a sub-network of the papers with the highest number of inter-citations (with a minimal in-degree of 28) was selected to perform a combination of network clustering and text mining to identify the paradigmatic research fronts and analyze their dynamics...
2017: PloS One
https://www.readbyqxmd.com/read/28542550/a-spatio-temporal-assessment-of-simian-human-immunodeficiency-virus-shiv-evolution-reveals-a-highly-dynamic-process-within-the-host
#14
Alison F Feder, Christopher Kline, Patricia Polacino, Mackenzie Cottrell, Angela D M Kashuba, Brandon F Keele, Shiu-Lok Hu, Dmitri A Petrov, Pleuni S Pennings, Zandrea Ambrose
The process by which drug-resistant HIV-1 arises and spreads spatially within an infected individual is poorly understood. Studies have found variable results relating how HIV-1 in the blood differs from virus sampled in tissues, offering conflicting findings about whether HIV-1 throughout the body is homogeneously distributed. However, most of these studies sample only two compartments and few have data from multiple time points. To directly measure how drug resistance spreads within a host and to assess how spatial structure impacts its emergence, we examined serial sequences from four macaques infected with RT-SHIVmne027, a simian immunodeficiency virus encoding HIV-1 reverse transcriptase (RT), and treated with RT inhibitors...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28532401/risk-reassurance-and-routine-a-qualitative-study-of-narrative-understandings-of-the-potential-for-hiv-self-testing-among-men-who-have-sex-with-men-in-england
#15
T Charles Witzel, Peter Weatherburn, Alison J Rodger, Adam H Bourne, Fiona M Burns
BACKGROUND: HIV testing has seen a rapid evolution over the last decade with multiple modalities now in use globally. In recent years HIV self-testing (HIVST) has been legalised in the UK paving the way for further expansion of testing. Interventions are delivered in particular social contexts which shape uptake. It is therefore important to understand how novel interventions are likely to be received by their intended users. This study aims to understand how HIVST compliments existing testing strategies considered or adopted by men who have sex with men (MSM)...
May 22, 2017: BMC Public Health
https://www.readbyqxmd.com/read/28529718/recent-advances-in-understanding-hiv-evolution
#16
REVIEW
Sophie M Andrews, Sarah Rowland-Jones
The human immunodeficiency virus (HIV) evolves rapidly owing to the combined activity of error-prone reverse transcriptase, recombination, and short generation times, leading to extensive viral diversity both within and between hosts. This diversity is a major contributing factor in the failure of the immune system to eradicate the virus and has important implications for the development of suitable drugs and vaccines to combat infection. This review will discuss the recent technological advances that have shed light on HIV evolution and will summarise emerging concepts in this field...
2017: F1000Research
https://www.readbyqxmd.com/read/28528522/reconstitution-inflammatory-syndrome-like-reactive-hemophagocytic-syndrome-associated-with-disseminated-histoplasmosis-in-a-hiv-patient
#17
REVIEW
Sandra M Gómez-Espejo, Julián Olalla-Sierra, Pilar Marí-Jiménez, Teresa Pereda-Salguero, Javier Pérez-Stachowski, Javier de-la-Torre-Lima, Alfonso Del-Arco-Jiménez, José L Prada-Pardal
We describe an unusual clinical association of disseminated histoplasmosis with reactive hemophagocytic syndrome. We report the case of a new HIV-positive patient with reconstitution inflammatory syndrome like reactive hemophagocytic syndrome associated with disseminated histoplasmosis. We describe the clinical case, the procedures performed, the treatment provided and the patient's evolution. A figure of liver biopsy Grocott's silver methenamine stain that shows lots of uniform ovoid yeasts in portal spaces' macrophages that supports the diagnosis of disseminated histoplasmosis in our case...
May 20, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28520969/cell-mediated-immunity-to-target-the-persistent-human-immunodeficiency-virus-reservoir
#18
James L Riley, Luis J Montaner
Effective clearance of virally infected cells requires the sequential activity of innate and adaptive immunity effectors. In human immunodeficiency virus (HIV) infection, naturally induced cell-mediated immune responses rarely eradicate infection. However, optimized immune responses could potentially be leveraged in HIV cure efforts if epitope escape and lack of sustained effector memory responses were to be addressed. Here we review leading HIV cure strategies that harness cell-mediated control against HIV in stably suppressed antiretroviral-treated subjects...
March 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28511559/migrating-microbes-what-pathogens-can-tell-us-about-population-movements-and-human-evolution
#19
Charlotte J Houldcroft, Jean-Baptiste Ramond, Riaan F Rifkin, Simon J Underdown
BACKGROUND: The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases...
May 16, 2017: Annals of Human Biology
https://www.readbyqxmd.com/read/28509569/hiv-1-crf07_bc-with-a-seven-amino-acid-deletion-in-the-gag-p6-region-dominates-in-hiv-1-infected-men-who-have-sex-with-men-in-china
#20
Yue Wu, Haiying Wang, Xuqi Ren, Zhengwei Wan, Guifang Hu, Shixing Tang
We examined sequence variation in the HIV-1 gag p6 region from 27 individuals infected with HIV-1 CRF07_BC. An additional 269 gag p6 sequences of CRF07_BC from the Los Alamos National Laboratory database were also analyzed. A unique deletion of seven amino acid (aa) (p6Δ7) (aa 30-36, PIDKELY, in the HXB2 genome) was observed to exist exclusively in CRF07_BC. Indeed, 54.1% (160/296) of the CRF07_BC sequences contained the p6Δ7 mutation. The prevalence of the p6Δ7 mutation was 37.2% (29/78) and 92.3% (48/52) in CRF07_BC-infected intravenous drug users and men who have sex with men (MSM), respectively...
May 16, 2017: AIDS Research and Human Retroviruses
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