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https://www.readbyqxmd.com/read/29343575/high-resolution-sequencing-of-viral-populations-during-early-siv-infection-reveals-evolutionary-strategies-for-rapid-escape-from-emerging-env-specific-antibody-responses
#1
Sergio Ita, Alison K Hill, Evan C Lam, Fay J Dufort, Xiao Yang, Ruchi Newman, Sivan Leviyang, Ismael B Fofana, Welkin E Johnson
Primate lentiviruses, including the human and simian immunodeficiency viruses (HIV and SIV), produce infections marked by persistent, ongoing viral replication. This occurs despite the presence of virus-specific adaptive immune responses, including antibodies targeting the viral envelope glycoprotein (Env), and evolution of antibody-escape variants is a well-documented feature of lentiviral infection. Here, we examined the evolutionary dynamics of the SIV env gene during early infection (≤ 29 weeks post-infection) in a cohort of four SIVmac251-infected rhesus macaques...
January 17, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29338056/context-dependent-autoprocessing-of-human-immunodeficiency-virus-type-1-protease-precursors
#2
ChihFeng Tien, Liangqun Huang, Susan M Watanabe, Jordan T Speidel, Carol A Carter, Chaoping Chen
HIV-1 protease autoprocessing is responsible for liberation of free mature protease (PR) from the Gag-Pol polyprotein precursor. A cell-based model system was previously developed to examine the autoprocessing mechanism of fusion precursors carrying the p6*-PR miniprecursor sandwiched between various proteins or epitopes. We here report that precursor autoprocessing is context-dependent as its activity and outcomes can be modulated by sequences upstream of p6*-PR. This was exemplified by the 26aa maltose binding protein (MBP) signal peptide (SigP) when placed at the N-terminus of a fusion precursor...
2018: PloS One
https://www.readbyqxmd.com/read/29333092/role-of-apobec3h-in-the-viral-control-of-hiv-elite-controller-patients
#3
José M Benito, Julia Hillung, Clara Restrepo, José M Cuevas, Agathe León, Ezequiel Ruiz-Mateos, Rosario Palacios-Muñoz, Miguel Górgolas, Rafael Sanjuán, Norma Rallón
Background APOBEC3H (A3H) gene presents variation at 2 positions (rs139297 and rs79323350) leading to a non-functional protein. So far, there is no information on the role played by A3H in spontaneous control of HIV. The aim of this study was to evaluate the A3H polymorphisms distribution in a well-characterized group of Elite Controller (EC) subjects. Methods We analyzed the genotype distribution of two different SNPs (rs139297 and rs79323350) of A3H in 30 EC patients and compared with 11 non-controller (NC) HIV patients...
2018: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29332615/hiv-epidemic-heterogeneity-in-zimbabwe-evidence-from-successive-demographic-and-health-surveys
#4
Zainab Oseni, Farah Seedat, Ngianga-Bakwin Kandala
Zimbabwe has one of the worst HIV epidemics in the world. This study investigated data from two successive Zimbabwe Demographic and Health Surveys (ZDHS) conducted in 2005-06 and 2010-11. A random representative sample of 30,000 men aged 15-59 and women aged 15-49 was selected from the two surveys. The HIV prevalence was mapped with a flexible, coherent regression framework using a geo-additive semi-parametric mixed model. HIV indicator prevalence maps were constructed at the regional level, and at the administrative level relevant for policy design, planning and decision-making...
January 15, 2018: Journal of Biosocial Science
https://www.readbyqxmd.com/read/29330173/seasonal-variations-in-tuberculosis-diagnosis-among-hiv-positive-individuals-in-southern-africa-analysis-of-cohort-studies-at-antiretroviral-treatment-programmes
#5
Marie Ballif, Kathrin Zürcher, Stewart E Reid, Andrew Boulle, Matthew P Fox, Hans W Prozesky, Cleophas Chimbetete, Marcel Zwahlen, Matthias Egger, Lukas Fenner
OBJECTIVES: Seasonal variations in tuberculosis diagnoses have been attributed to seasonal climatic changes and indoor crowding during colder winter months. We investigated trends in pulmonary tuberculosis (PTB) diagnosis at antiretroviral therapy (ART) programmes in Southern Africa. SETTING: Five ART programmes participating in the International Epidemiology Database to Evaluate AIDS in South Africa, Zambia and Zimbabwe. PARTICIPANTS: We analysed data of 331 634 HIV-positive adults (>15 years), who initiated ART between January 2004 and December 2014...
January 11, 2018: BMJ Open
https://www.readbyqxmd.com/read/29330056/growth-scaling-for-the-early-dynamics-of-hiv-aids-epidemics-in-brazil-and-the-influence-of-socio-demographic-factors
#6
L Dinh, G Chowell, R Rothenberg
The early dynamics of an infectious disease outbreak can be affected by various factors including the transmission mode of the disease and host-specific factors. While recent works have highlighted the presence of sub-exponential growth patterns during the early phase of epidemics, empirical studies examining the contribution of different factors to early epidemic growth dynamics are lacking. Here we aim to characterize and explain the early incidence growth patterns of local HIV/AIDS epidemics in Brazil as a function of socio-demographic factors...
January 9, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29329426/a-practical-guide-to-estimating-the-heritability-of-pathogen-traits
#7
Venelin Mitov, Tanja Stadler
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens...
January 9, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29325426/naturally-occurring-mutations-in-hiv-1-crf01_ae-capsid-affect-viral-sensitivity-to-restriction-factors
#8
Emi E Nakayama, Akatsuki Saito, Tahmina Sultana, Zhuan Jin, Kyotaro Nohata, Masato Shibata, Miho Hosoi, Kazushi Motomura, Tatsuo Shioda, Somchai Sangkitporn, Ruangchai Loket, Siriphan Saeng-Aroon
TRIM5α and MxB are known as restriction factors that inhibit the early step of intracellular HIV-1 replication cycle. Both factors are believed to interact with the incoming virus core to suppress HIV-1 infection. The extreme diversity of HIV-1 is thought to be a consequence of its propensity to mutate to escape immune responses and host restriction factors. We recently determined the capsid sequences for 144 HIV-1 CRF01_AE viruses obtained in Thailand from 2005 to 2011. In the present study, we further analyzed the amino acid variations among the capsid sequences of 204 HIV-1 CRF01_AE obtained in Thailand and China, including 84 of the aforementioned 144 viruses, to detect mutations permitting escape from restriction by host factors...
January 12, 2018: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/29322922/analysis-of-viral-diversity-for-vaccine-target-discovery
#9
Asif M Khan, Yongli Hu, Olivo Miotto, Natascha M Thevasagayam, Rashmi Sukumaran, Hadia Syahirah Abd Raman, Vladimir Brusic, Tin Wee Tan, J Thomas August
BACKGROUND: Viral vaccine target discovery requires understanding the diversity of both the virus and the human immune system. The readily available and rapidly growing pool of viral sequence data in the public domain enable the identification and characterization of immune targets relevant to adaptive immunity. A systematic bioinformatics approach is necessary to facilitate the analysis of such large datasets for selection of potential candidate vaccine targets. RESULTS: This work describes a computational methodology to achieve this analysis, with data of dengue, West Nile, hepatitis A, HIV-1, and influenza A viruses as examples...
December 21, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/29321314/hla-class-i-downregulation-by-hiv-1-variants-from-subtype-c-transmission-pairs
#10
Zachary Ende, Martin J Deymier, Daniel T Claiborne, Jessica L Prince, Daniela C Mónaco, William Kilembe, Susan A Allen, Eric Hunter
HIV-1 downregulates HLA-A and HLA-B from the surface of infected cells primarily to evade CD8 T cell recognition. HLA-C was thought to remain on the cell surface and bind inhibitory killer immunoglobulin-like receptors, preventing NK cell-mediated suppression. However, a recent study found HIV-1 primary viruses have the capacity to downregulate HLA-C. The goal of this study was to assess the heterogeneity of HLA-A, HLA-B and HLA-C downregulation among full-length primary viruses from six chronically infected and six newly infected individuals from transmission pairs, and to determine whether transmitted/founder variants exhibit common HLA class I downregulation characteristics...
January 10, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29320814/genotypic-identification-of-cystoisospora-in-immunocompromised-patients-using-tm-variation-analysis
#11
Maha M A Basyoni, Hany Ahmed Fouad Elghobary
Cystoisospora is responsible for morbidity in immunocompromised patients. PCR is sensitive for diagnosing Cystoisospora; however, it needs reevaluation for differential molecular diagnosis of cystoisosporiasis. We aimed at evaluating melting curve analysis (MCA) after real-time PCR (qPCR) in diagnosis and genotyping of Cystoisospora as an alternative to conventional PCR. We included 293 diarrheic stool samples of patients attending the Department of Clinical Oncology and Nuclear Medicine of Cairo University Hospitals, Egypt...
December 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/29318924/how-to-live-a-good-life-aging-and-hiv-testing-in-rural-south-africa
#12
Enid Schatz, Brian Houle, Sanyu A Mojola, Nicole Angotti, Jill Williams
OBJECTIVE: The African HIV epidemic is aging, yet HIV testing behavior studies either exclude older persons or include too few to say much about age differences. METHOD: Strategically combining focus group interviews (participants in 40s/50s/60s-plus age groups) and survey data from rural South Africa (where HIV prevalence peaks in the late 30s, but continues to be over 10% into the late 60s), we examine gender and life course variation, motivations, and barriers in HIV testing...
January 1, 2018: Journal of Aging and Health
https://www.readbyqxmd.com/read/29315954/development-and-validation-of-an-assay-to-analyze-atazanavir-in-human-hair-via-liquid-chromatography-tandem-mass-spectrometry-lc-ms-ms
#13
Nhi Phung, Karen Kuncze, Hideaki Okochi, Alexander Louie, Leslie Z Benet, Igho Ofokotun, David W Haas, Judith S Currier, Tariro D Chawana, Anandi N Sheth, Peter Bacchetti, Monica Gandhi, Howard Horng
Assays to quantify antiretrovirals in hair samples are increasingly used to monitor adherence and exposure in both HIV prevention and treatment studies. Atazanavir (ATV) is a protease inhibitor used in combination antiretroviral therapy (ART). We developed and validated a liquid chromatography tandem mass spectrometry (LC-MS/MS)-based method to quantify ATV in human hair, per the NIH Division of AIDS' Clinical Pharmacology Quality Assurance (CPQA) program and the FDA bioanalytical method validation guidelines...
January 9, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29315303/genome-wide-comparison-of-ethiopian-leishmania-donovani-strains-reveals-differences-potentially-related-to-parasite-survival
#14
Arie Zackay, James A Cotton, Mandy Sanders, Asrat Hailu, Abedelmajeed Nasereddin, Alon Warburg, Charles L Jaffe
Leishmania donovani is the main cause of visceral leishmaniasis (VL) in East Africa. Differences between northern Ethiopia/Sudan (NE) and southern Ethiopia (SE) in ecology, vectors, and patient sensitivity to drug treatment have been described, however the relationship between differences in parasite genotype between these two foci and phenotype is unknown. Whole genomic sequencing (WGS) was carried out for 41 L. donovani strains and clones from VL and VL/HIV co-infected patients in NE (n = 28) and SE (n = 13)...
January 9, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29314670/eliminating-hepatitis-c-virus-as-a-public-health-threat-among-hiv-positive-men-who-have-sex-with-men-a-multi-modelling-approach-to-understand-differences-in-sexual-risk-behaviour
#15
Nick Scott, Mark Stoové, David P Wilson, Olivia Keiser, Carol El-Hayek, Joseph Doyle, Margaret Hellard
INTRODUCTION: Outbreaks of hepatitis C virus (HCV) infections among HIV-positive men who have sex with men (MSM) have been observed globally. Using a multi-modelling approach we estimate the time and number of direct-acting antiviral treatment courses required to achieve an 80% reduction in HCV prevalence among HIV-positive MSM in the state of Victoria, Australia. METHODS: Three models of HCV transmission, testing and treatment among MSM were compared: a dynamic compartmental model; an agent-based model (ABM) parametrized to local surveillance and behavioural data ("ABM1"); and an ABM with a more heterogeneous population ("ABM2") to determine the influence of extreme variations in sexual risk behaviour...
January 2018: Journal of the International AIDS Society
https://www.readbyqxmd.com/read/29304164/influence-of-peer-support-on-hiv-sti-prevention-and-safety-amongst-international-migrant-sex-workers-a-qualitative-study-at-the-mexico-guatemala-border
#16
Belen Febres-Cordero, Kimberly C Brouwer, Teresita Rocha-Jimenez, Carmen Fernandez-Casanueva, Sonia Morales-Miranda, Shira M Goldenberg
BACKGROUND: Migrant women engaged in precarious employment, such as sex work, frequently face pronounced social isolation alongside other barriers to health and human rights. Although peer support has been identified as a critical HIV and violence prevention intervention for sex workers, little is known about access to peer support or its role in shaping health and social outcomes for migrant sex workers. This article analyses the role of peer support in shaping vulnerability and resilience related to HIV/STI prevention and violence among international migrant sex workers at the Mexico-Guatemala border...
2018: PloS One
https://www.readbyqxmd.com/read/29295533/hiv-1-subtypes-and-5-ltr-leader-sequence-variants-correlate-with-seroconversion-status-in-pumwani-sex-worker-cohort
#17
Raghavan Sampathkumar, Joel Scott-Herridge, Binhua Liang, Joshua Kimani, Francis A Plummer, Ma Luo
Within the Pumwani sex worker cohort, a subgroup remains seronegative, despite frequent exposure to HIV-1; some of them seroconverted several years later. This study attempts to identify viral variations in 5'LTR-leader sequences (5'LTR-LS) that might contribute to the late seroconversion. The 5'LTR-LS contains sites essential for replication and genome packaging, viz, primer binding site (PBS), major splice donor (SD), and major packaging signal (PS). The 5'LTR-LS of 20 late seroconverters (LSC) and 122 early seroconverters (EC) were amplified, cloned, and sequenced...
December 23, 2017: Viruses
https://www.readbyqxmd.com/read/29295020/disclosing-sex-trading-histories-to-providers-barriers-and-facilitators-to-navigation-of-social-services-among-women-impacted-by-commercial-sexual-exploitation
#18
Lara Gerassi, Tonya E Edmond, Vanessa Fabbre, Abby Howard, Andrea J Nichols
Sex trafficking and commercial sexual exploitation (CSE) can lead to devastating health and mental health consequences for women, such as elevated rates of substance use, trauma, posttraumatic stress disorder, depression, sexually transmitted infections (STIs), and HIV. Consequently, engagement with services that address addiction, mental health, and housing, and provide general advocacy is critically important to women's increased safety, stabilization, and quality of life. The purpose of this study is to identify perceived barriers and facilitators to service access and engagement with social services among women involved in CSE...
December 1, 2017: Journal of Interpersonal Violence
https://www.readbyqxmd.com/read/29280767/sexual-networks-of-racially-diverse-young-msm-differ-in-racial-homophily-but-not-concurrency
#19
Patrick Janulis, Gregory Phillips, Michelle Birkett, Brian Mustanski
BACKGROUND: Substantial racial disparities exist in HIV infection among young men who have sex with men (YMSM). However, evidence suggests Black YMSM do not engage in greater levels of risk behavior. Sexual networks may help explain this paradox. This study utilized egocentric exponential random graph models (ERGMs) to examine variation in concurrency (i.e., 2 or more simultaneous partners) and homophily (i.e., same race/ethnicity partners) across race/ethnicity groups in a diverse sample of YMSM...
December 26, 2017: Journal of Acquired Immune Deficiency Syndromes: JAIDS
https://www.readbyqxmd.com/read/29277535/determination-of-dolutegravir-s-unbound-fraction-in-human-plasma-using-validated-equilibrium-dialysis-and-lc-ms-ms-methods
#20
David Metsu, Thomas Lanot, François Fraissinet, Mélanie Picot, Didier Concordet, Marion Cabrol, Frédérique Dubois-Galopin, Etienne Chatelut, Pierre Delobel, Peggy Gandia
Assessment of the unbound pharmacologically active fraction (fu; as the ratio of unbound to total concentration) of dolutegravir could improve therapeutic drug monitoring (TDM) in patients that experience virological failure or toxicity, despite receiving adequate total concentrations. This study evaluated (i) dolutegravir's fu through equilibrium dialysis (ED), (ii) the pre-analytical parameters that influence fu, and (iii) fu's inter-individual variability in HIV patients. Validation of the LC-MS/MS method followed FDA guidelines...
December 22, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
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