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HIV evolution

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https://www.readbyqxmd.com/read/28520969/cell-mediated-immunity-to-target-the-persistent-human-immunodeficiency-virus-reservoir
#1
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
#2
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
#3
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
https://www.readbyqxmd.com/read/28507544/within-epitope-interactions-can-bias-ctl-escape-estimation-in-early-hiv-infection
#4
Victor Garcia, Marcus W Feldman
As human immunodeficiency virus (HIV) begins to replicate within hosts, immune responses are elicited against it. Escape mutations in viral epitopes-immunogenic peptide parts presented on the surface of infected cells-allow HIV to partially evade these responses, and thus rapidly go to fixation. The faster they go to fixation, i.e., the higher their escape rate, the larger the selective pressure exerted by the immune system is assumed to be. This relation underpins the rationale for using escapes to assess the strength of immune responses...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28502791/single-strand-consensus-sequencing-reveals-that-hiv-type-but-not-subtype-significantly-impacts-viral-mutation-frequencies-and-spectra
#5
Jonathan M O Rawson, Daryl M Gohl, Sean R Landman, Megan E Roth, Morgan E Meissner, Tara S Peterson, James S Hodges, Kenneth B Beckman, Louis M Mansky
A long-standing question of human immunodeficiency virus (HIV) genetic variation and evolution has been whether differences exist in mutation rate and/or mutation spectra among HIV types (i.e., HIV-1 versus HIV-2) as well as among HIV groups (i.e., HIV-1 groups M-P and HIV-2 groups A-H) and HIV-1 Group M subtypes (i.e., subtypes A-D, F-H, and J-K). To address this, a new single-strand consensus sequencing assay was developed for the determination of HIV mutation frequencies and spectra using the Illumina sequencing platform...
May 11, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28502523/human-immunodeficiency-virus-diagnostic-approach
#6
REVIEW
Jeannette Guarner
First descriptions of acquired immunodeficiency syndrome appeared in 1981. Four years later the causative agent was cultured which lead to development and production of tests that helped healthcare providers to identify persons living with HIV. Currently, diagnosis of HIV is performed with fourth generation immunoassays (those that detect p24 antigen together with IgM and IgG antibodies to HIV-1 and -2) which if positive need to be followed by an assay that can differentiate between HIV-1 and HIV-2 viruses...
April 8, 2017: Seminars in Diagnostic Pathology
https://www.readbyqxmd.com/read/28497113/toward-a-cure-does-host-immunity-play-a-role
#7
Jielin Zhang, Clyde S Crumpacker
Three decades of research on human immunodeficiency virus (HIV) and AIDS reveal that the human body has developed through evolution a genome immune system embodying epigenetic regulation against pathogenic nucleic acid invasion. In HIV infection, this epigenetic regulation plays a cardinal role in HIV RNA production that silences HIV transcription at a molecular (RNA) level, controls viral load at a cellular (biological) level, and governs the viremic stage of AIDS at the clinical (patient) level. Even though the human genome is largely similar among humans and HIV is a single viral species, human hosts show significant differences in viral RNA levels, ranging from cell to organ to individual and expressed as elite controllers, posttreatment controllers, and patients with AIDS...
March 2017: MSphere
https://www.readbyqxmd.com/read/28484443/impact-of-genetic-variations-in-hiv-1-tat-on-ltr-mediated-transcription-via-tar-rna-interaction
#8
Larance Ronsard, Nilanjana Ganguli, Vivek K Singh, Kumaravel Mohankumar, Tripti Rai, Subhashree Sridharan, Sankar Pajaniradje, Binod Kumar, Devesh Rai, Suhnrita Chaudhuri, Mohane S Coumar, Vishnampettai G Ramachandran, Akhil C Banerjea
HIV-1 evades host defense through mutations and recombination events, generating numerous variants in an infected patient. These variants with an undiminished virulence can multiply rapidly in order to progress to AIDS. One of the targets to intervene in HIV-1 replication is the trans-activator of transcription (Tat), a major regulatory protein that transactivates the long terminal repeat promoter through its interaction with trans-activation response (TAR) RNA. In this study, HIV-1 infected patients (n = 120) from North India revealed Ser46Phe (20%) and Ser61Arg (2%) mutations in the Tat variants with a strong interaction toward TAR leading to enhanced transactivation activities...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28482929/ivermectin-induced-steven-johnsons-syndrome-case-report
#9
Desmond Aroke, Diego Nitcheu Tchouakam, Alexis Tazinya Awungia, Sylvester Yari Mapoh, Stewart Ndutard Ngassa, Benjamin Momo Kadia
BACKGROUND: Stevens-Johnson syndrome is one of the manifestations of mucocutaneous adverse drug reactions. Although antimicrobials are responsible for greater than 50% of these adverse drug reactions, there is no documented case implicating ivermectin as the culprit. A 38 year old adult Cameroonian male presented to our health facility with facial rash, painful oral sores, black eschars on lips and red tearing eyes 3 days following ingestion of ivermectin received during a nationwide anti-filarial campaign...
May 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28476627/-the-impact-of-mycobacterium-tuberculosis-immune-evasion-on-protective-immunity-implications-for-tb-vaccine-design-meeting-report
#10
Cesar Boggiano, Katrin Eichelberg, Lakshmi Ramachandra, Jaqueline Shea, Lalita Ramakrishnan, Samuel Behar, Joel D Ernst, Steven A Porcelli, Markus Maeurer, Hardy Kornfeld
Tuberculosis (TB) is the major cause of death from infectious diseases around the world, particularly in HIV infected individuals. TB vaccine design and development have been focused on improving Bacille Calmette-Guérin (BCG) and evaluating recombinant and viral vector expressed Mycobacterium tuberculosis (Mtb) proteins, for boosting BCG-primed immunity, but these approaches have not yet yielded significant improvements over the modest effects of BCG in protecting against infection or disease. On March 7-8, 2016, the National Institute of Allergy and Infectious Diseases (NIAID) convened a workshop on "The Impact of Mtb Immune Evasion on Protective Immunity: Implications for TB Vaccine Design" with the goal of defining immune mechanisms that could be targeted through novel research approaches, to inform vaccine design and immune therapeutic interventions for prevention of TB...
May 2, 2017: Vaccine
https://www.readbyqxmd.com/read/28474534/evolution-of-hiv-1-surveillance-drug-resistance-mutations-over-ten-years-in-new-south-wales-australia
#11
Angie Pinto, Alex Carrera, Hanan Salem, Kiran Thapa, Ansari Shaik, Kathy Petoumenos, Philip Cunningham, Roger Garsia, Dominic Dwyer, David A Cooper, Anthony D Kelleher
New South Wales (NSW) has the greatest burden of HIV in Australia, with 2012 and 2013 recording the highest rates of new diagnoses in twenty years. Concurrently, there has been significant changes in antiretorviral treatments and testing paradigms. We compiled a statewide resistance database to characterize changes in HIV-1 resistance mutations over time. Genotypic antiretroviral resistance testing (GART) was performed on request at three reference laboratories using commercial and in house methods. 7629 HIV-1 polymerase sequences obtained from GART from 2004-2013 were retrospectively collated, reformatted, de-identified and analysed using Stanford HIVdb program 7...
May 5, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28466391/mechanisms-of-hiv-1-control
#12
REVIEW
Mary Soliman, Geetha Srikrishna, Ashwin Balagopal
PURPOSE OF REVIEW: HIV-1 infection is of global importance, and still incurs substantial morbidity and mortality. Although major pharmacologic advances over the past two decades have resulted in remarkable HIV-1 control, a cure is still forthcoming. One approach to a cure is to exploit natural mechanisms by which the host restricts HIV-1. Herein, we review past and recent discoveries of HIV-1 restriction factors, a diverse set of host proteins that limit HIV-1 replication at multiple levels, including entry, reverse transcription, integration, translation of viral proteins, and packaging and release of virions...
June 2017: Current HIV/AIDS Reports
https://www.readbyqxmd.com/read/28464889/highly-divergent-patterns-of-genetic-diversity-and-evolution-in-proviral-quasispecies-from-hiv-controllers
#13
Suwellen S D de Azevedo, Diogo Gama Caetano, Fernanda H Côrtes, Sylvia L M Teixeira, Karina Dos Santos Silva, Brenda Hoagland, Beatriz Grinsztejn, Valdilea G Veloso, Mariza G Morgado, Gonzalo Bello
BACKGROUND: Ongoing intra-host HIV-1 evolution has been shown in individuals that naturally suppress the viremia to low levels (HIV controllers) by the analysis of the RNA in plasma compartment. Detection of evolution at the DNA proviral compartment in HIV controllers, however, has been more challenging and the precise correlation between the systemic viral suppression level and rate of reservoir's reseeding in those individuals is not fully understood. In this sense, we examined the proviral DNA quasispecies by single genome amplification of the env gene in a cohort of 23 HIV controllers from Brazil, divided in three groups, according to the level of systemic viral suppression: (1) elite controllers with persistent undetectable viral load (PEC, n = 6); (2) elite controllers with occasional episodes of transient (51-400 copies/mL) viremia (EEC, n = 7); and (3) viremic controllers with persistent low-level (80-2000 copies/mL) viremia (VC, n = 10)...
May 2, 2017: Retrovirology
https://www.readbyqxmd.com/read/28462923/similarity-in-viral-and-host-promoters-couples-viral-reactivation-with-host-cell-migration
#14
Kathrin Bohn-Wippert, Erin N Tevonian, Melina R Megaridis, Roy D Dar
Viral-host interactomes map the complex architecture of an evolved arms race during host cell invasion. mRNA and protein interactomes reveal elaborate targeting schemes, yet evidence is lacking for genetic coupling that results in the co-regulation of promoters. Here we compare viral and human promoter sequences and expression to test whether genetic coupling exists and investigate its phenotypic consequences. We show that viral-host co-evolution is imprinted within promoter gene sequences before transcript or protein interactions...
May 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28462780/-african-histoplamosis-a-report-of-three-pediatric-cases
#15
REVIEW
J R Mabiala Babela, C Mboutol Mandavo, R Nika Evrard, B Ossibi Ibara, L Lamah, L C Ollandzobo Ikobo, A Mouko, J F Peko
Histoplasmosis duboisii (Histoplasma capsulatum var duboisii) is uncommon disease especially in children. It is observed in Africa where the incidence is unknown. The authors report a series of three pediatric cases. The report concerned 2 girls and one boy who were 3, 9 and 4 year-old, respectively. Symptoms evolved for more than two months in each case. At admission, we found fever and poor general condition. Observed lesions were lymphnodes localisation disseminated (cases 1 and 2), subcutaneous (cold abscess) and cutaneous simulating molluscum contagiosum (case 2), osteoarticular (cases 2 and 3), abdominal including peritoneal and hepatosplenic (case 1)...
April 24, 2017: Journal de Mycologie Médicale
https://www.readbyqxmd.com/read/28461838/bilateral-chorioretinal-scars-in-a-child-case-report
#16
Tomi Anca, Stefan Irina
The eye manifestations of intrauterine infections are multiple, but chorioretinal scars and/or active chorioretinitis are the most frequently reported. When associated with other systemic manifestations of the infection, the diagnosis becomes more obvious, but when eye involvement is the only abnormality, etiology often remains uncertain. We are presenting the case of an 8-year-old female patient whose fundus lesions revealed an unusual choroidoretinopathy, associated with cataract in one eye. Her general examination and her medical history were unremarkable...
June 2016: Mædica
https://www.readbyqxmd.com/read/28458914/in-vivo-mutation-rates-and-the-landscape-of-fitness-costs-of-hiv-1
#17
Fabio Zanini, Vadim Puller, Johanna Brodin, Jan Albert, Richard A Neher
Mutation rates and fitness costs of deleterious mutations are difficult to measure in vivo but essential for a quantitative understanding of evolution. Using whole genome deep sequencing data from longitudinal samples during untreated HIV-1 infection, we estimated mutation rates and fitness costs in HIV-1 from the dynamics of genetic variation. At approximately neutral sites, mutations accumulate with a rate of 1.2 × 10(-5) per site per day, in agreement with the rate measured in cell cultures. We estimated the rate from G to A to be the largest, followed by the other transitions C to T, T to C, and A to G, while transversions are less frequent...
January 2017: Virus Evolution
https://www.readbyqxmd.com/read/28454556/molecular-and-epidemiological-characterization-of-hiv-1-subtypes-among-libyan-patients
#18
Mohamed A Daw, Abdallah El-Bouzedi, Mohamed O Ahmed, Aghnyia A Dau
BACKGROUND: The epidemiological and clinical aspects of human immunodeficiency virus subtypes are of great interest worldwide. These subtypes are rarely studied in North African countries. Libya is a large country with the longest coast on the Mediterranean Sea, facing the Southern European countries. Studies on the characterization of HIV-1 subtypes are limited in Libya. This study aimed to determine the magnitude of the HIV problem among the Libyan population and to better understand the genetic diversity and the epidemiologic dynamics of HIV 1, as well as to correlate that with the risk factors involved...
April 28, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28453022/-evolution-of-epidemiological-and-clinical-characteristics-of-adults-patients-belonging-to-the-national-program-at-start-of-antiretroviral-therapy-in-the-chilean-aids-cohort-2001-2015
#19
Carlos Beltrán, Pedro Zitko, Marcelo Wolff, Fernando Bernal, Alicia Asenjo, Ana M Fernández, Ana Miles, Elizabeth Barthel, Gonzalo Wilson
BACKGROUND: Chilean AIDS Cohort is the oldest and extensive in Latin America and one of most numerous and with longer follow up time to international level. Records information from 14,873 patients out of approximately 22,000 in antiretroviral therapy in the public system and its results have allowed to know the national reality and have contributed to the adoption of public policies. AIM: To describe the demographic, clinical and immunological characteristics of patients who have started ART in Chile and its evolution over the past 15 years...
October 2016: Revista Chilena de Infectología: órgano Oficial de la Sociedad Chilena de Infectología
https://www.readbyqxmd.com/read/28445881/absence-of-decline-of-kidney-function-in-human-immunodeficiency-virus-infected-patients-under-routine-clinical-management
#20
Julie Boucquemont, Sylvie Lawson-Ayayi, Claire Rigothier, Fabrice Bonnet, Cécile Proust-Lima, Didier Neau, Carine Greib, Ghada Miremont-Salamé, François Dabis, Michel Dupon, Frédéric-Antoine Dauchy
BACKGROUND: Since the introduction of antiretroviral therapy (ART), human immunodeficiency virus (HIV)-infected patients have a drastically improved prognosis but at the same time they are also more affected by non-HIV related complications, such as chronic kidney disease. The objective of our study was to investigate the effect of proteinuria and tenofovir (TDF)-containing ART regimens on the temporal evolution of estimated glomerular filtration rate (eGFR). METHODS: Between April 2008 and October 2012, we enrolled 395 patients with a complete renal evaluation among patients from the ANRS C03 Aquitaine cohort, a prospective hospital-based cohort of HIV-1-infected patients under routine clinical management in southwestern France...
April 26, 2017: Nephron
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