Time-scale of minor HIV-1 complex circulating recombinant forms from Central and West Africa

Table S1. Sequences reclassified in this study. (PDF 75 kb

ANÁLISE DO USO E OCUPAÇÃO DO SOLO NAS ÁREAS DE PRESERVAÇÃO PERMANENTE DA MICROBACIA RIBEIRÃO BONITO, APOIADA EM TÉCNICAS DE GEOPROCESSAMENTO.

Com o crescimento populacional e o consumo exacerbado, os recursos naturais são constantementeexplorados. As matas ciliares podem ser consideradas um dos recursos mais ameaçado e sujeito adegradação. No intuito de monitorar os problemas ambientais, os SIGs, aliados as técnicas degeoprocessamento, apresentam grande potencialidade. Estes permitem o acúmulo e manipulação degrande número de informações, bem como a representação cartográfica dessas variáveis, tornando-seessa técnica um excelente meio para analise do uso e ocupação das terras, no caso, nas Áreas dePreservação Permanente. O objetivo foi realizar o mapeamento das APPs da microbacia do RibeirãoBonito, e identificar os diferentes usos e ocupações nestas áreas. Através das técnicas degeoprocessamento os usos da terra, foram delimitados e mapeados. Foram utilizadas as imagens desatélite ALOS do sensor PRISM (2,5 m de resolução), cartas topográficas na escala de 1: 50.000. Parao processamento das imagens, foram utilizados os SIGs ArcGIS 9.3.1 e Idrisi Taiga. O produto finalresultou em mapas de uso da terra em APP, e de uso adequado e inadequado das terras, revelando opredomínio de condições adequadas de uso, porém com a presença de impactos ambientais, comoerosões e assoreamento dos rios e nascentes

Proviral Quasispecies Diversity Is Not Associated With Virologic Breakthrough or CD4+ T Cell Loss in HIV-1 Elite Controllers

Elite controllers (EC) are able to control HIV-1 replication to extremely low levels (<50 HIV-1 RNA copies/mL) in the absence of antiretroviral therapy. However, some EC experience CD4+ T cell loss and/or lose their ability to control HIV-1 over the course of infection. High levels of HIV-1 env proviral diversity, activated T cells and proinflammatory cytokines were pointed out as relevant biomarkers for detection of EC at risk of virologic/immunologic progression. The aim of this study was to assess the importance of proviral diversity as a prognostic marker of virologic and/or immunologic progression in EC. To this end, we analyzed plasma viremia, total HIV DNA levels, T cells dynamics, and activation/inflammatory biomarkers in EC with low (ECLD = 4) and high (ECHD = 6) HIV-1 env diversity. None of ECLD and ECHD subjects displayed evidence of immunologic progression (decrease in absolute and percentage of CD4+ T cells) and only one ECHD subject presented virologic progression (≥2 consecutive viral loads measurements above the detection limit) 2–5 years after determination of proviral env diversity. Despite differences in proviral genetic diversity, the ECLD and ECHD subgroups displayed comparable levels of total cell-associated HIV DNA, activated CD8+ T (CD38+HLA-DR+) cells and plasmatic inflammatory biomarkers (IP-10, IL-18, RANTES, PDGF-AA, and CTACK). These results indicate that the genetic diversity of the HIV-1 proviral reservoir is not a surrogate marker of residual viral replication, immune activation or inflammation, nor an accurate biomarker for the prediction of virologic breakthrough or CD4+ T cells loss in EC

Reduction of HIV-1 Reservoir Size and Diversity After 1 Year of cART Among Brazilian Individuals Starting Treatment During Early Stages of Acute Infection

The aim of early combined antiretroviral therapy (cART) of HIV is to limit the seeding of the viral reservoir during the initial phase of infection and, consequently, decrease intrahost viral diversity. Here, we assessed the effect of early cART on size and complexity of the proviral reservoir. Peripheral blood mononuclear cell (PBMC) and plasma samples were obtained from ten HIV-infected Brazilian individuals diagnosed at the acute phase of infection, before (PREART) and 12 months (M12ART) after suppressive cART. HIV proviral reservoir size was determined by quantitative real-time PCR; intrahost viral diversity of the env C2-V3 region was assessed by single genome amplification or next-generation sequencing in PBMC and plasma, respectively. Mean nucleotide diversity (π) and normalized Shannon entropy (HSN) were used to infer the complexity of the viral population. Compared to PREART, M12ART saw an immunological recovery with a gain of ∼200 CD4+ T cells (P = 0.008) and a normalization of the CD4/CD8 ratio [1.0 (IQR: 0.88–1.18), P = 0.016], as well as a significant decrease in HIV-1 RNA (∼4 log, P = 0.004) and DNA (∼1 log, P = 0.002) levels. The median time to achieve viral suppression was 3 months (IQR: 2.8–5.8 months). The high intermixing between sequences from both visits suggests that the HIV-1 DNA reservoir remained remarkably stable under cART. After 1 year of cART, there was a minor reduction in proviral π (PreART = 0.20 vs. M12ART = 0.10; P = 0.156) but a significant decrease in HSN (PreART = 0.41 vs. M12ART = 0.25; P = 0.019). We found no correlation between π or HSN at PreART and the rate of HIV DNA decay, T CD4+ counts, or CD4/CD8 ratio at M12ART. Based on a small cohort of Brazilian infected individuals under early cART and analyses of the env region, 1 year of follow-up suggested a reservoir size reduction, allowed a significant decrease of HIV-1 complexity, and achieved immunological restoration regardless of the initial HIV-1 plasma viral load, CD4+ T cell counts, or HIV-1 subtype. However, further studies in the Brazilian setting aiming a longer follow-up and larger cohort are required in this field

Measurement of the correlation between flow harmonics of different order in lead-lead collisions at √sNN = 2.76 TeV with the ATLAS detector

Correlations between the elliptic or triangular flow coefficients vm (m=2 or 3) and other flow harmonics vn (n=2 to 5) are measured using √sNN=2.76 TeV Pb+Pb collision data collected in 2010 by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 7 μb−1. The vm−vn correlations are measured in midrapidity as a function of centrality, and, for events within the same centrality interval, as a function of event ellipticity or triangularity defined in a forward rapidity region. For events within the same centrality interval, v3 is found to be anticorrelated with v2 and this anticorrelation is consistent with similar anticorrelations between the corresponding eccentricities, ε2 and ε3. However, it is observed that v4 increases strongly with v2, and v5 increases strongly with both v2 and v3. The trend and strength of the vm−vn correlations for n=4 and 5 are found to disagree with εm−εn correlations predicted by initial-geometry models. Instead, these correlations are found to be consistent with the combined effects of a linear contribution to vn and a nonlinear term that is a function of v22 or of v2v3, as predicted by hydrodynamic models. A simple two-component fit is used to separate these two contributions. The extracted linear and nonlinear contributions to v4 and v5 are found to be consistent with previously measured event-plane correlations

Measurements of fiducial cross-sections for t\bart production with one or two additional b-jets in pp collisions at √s =8 TeVusing the ATLAS detector

Fiducial cross-sections for $t\bar{t}$ production with one or two additional $b$-jets are reported, using an integrated luminosity of 20.3 fb$^{-1}$ of proton--proton collisions at a centre-of-mass energy of 8 TeV at the Large Hadron Collider, collected with the ATLAS detector. The cross-section times branching ratio for $t\bar{t}$ events with at least one additional $b$-jet is measured to be 950 $\pm$ 70 (stat.) $^{+240}_{-190}$ (syst.) fb in the lepton-plus-jets channel and 50 $\pm$ 10 (stat.) $^{+15}_{-10}$ (syst.) fb in the $e \mu$ channel. The cross-section times branching ratio for events with at least two additional $b$-jets is measured to be 19.3 $\pm$ 3.5 (stat.) $\pm$ 5.7 (syst.) fb in the dilepton channel ($e \mu$,\,$\mu\mu$, and \,$ee$) using a method based on tight selection criteria, and 13.5 $\pm$ 3.3 (stat.) $\pm$ 3.6 (syst.) fb using a looser selection that allows the background normalisation to be extracted from data. The latter method also measures a value of 1.30 $\pm$ 0.33 (stat.) $\pm$ 0.28 (syst.)\% for the ratio of $t\bar{t}$ production with two additional $b$-jets to $t\bar{t}$ production with any two additional jets. All measurements are in good agreement with recent theory predictions.Comment: 41 pages plus author list + cover page (58 total), 9 Figures, 16 tables, submitted to EPJC, all figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/TOPQ-2014-10

Search for invisible particles produced in association with single-top-quarks in proton–proton collisions at √s = 8 TeV with the ATLAS detector

A search for the production of single-top-quarks in association with missing energy is performed in proton– proton collisions at a centre-of-mass energy of √s = 8 TeV with the ATLAS experiment at the large hadron collider using data collected in 2012, corresponding to an integrated luminosity of 20.3 fb−1. In this search, the W boson from the top quark is required to decay into an electron or a muon and a neutrino. No deviation from the standard model prediction is observed, and upper limits are set on the production cross-section for resonant and non-resonant production of an invisible exotic state in association with a right-handed top quark. In the case of resonant production, for a spin-0 resonance with a mass of 500 GeV, an effective coupling strength above 0.15 is excluded at 95 % confidence level for the top quark and an invisible spin-1/2 state with mass between 0 and 100 GeV. In the case of non-resonant production, an effective coupling strength above 0.2 is excluded at 95 % confidence level for the top quark and an invisible spin-1 state with mass between 0 and 657 GeV

Genome sequencing reveals Zika virus diversity and spread in the Americas

Although the recent Zika virus (ZIKV) epidemic in the Americas and its link to birth defects have attracted a great deal of attention, much remains unknown about ZIKV disease epidemiology and ZIKV evolution, in part owing to a lack of genomic data. Here we address this gap in knowledge by using multiple sequencing approaches to generate 110 ZIKV genomes from clinical and mosquito samples from 10 countries and territories, greatly expanding the observed viral genetic diversity from this outbreak. We analysed the timing and patterns of introductions into distinct geographic regions; our phylogenetic evidence suggests rapid expansion of the outbreak in Brazil and multiple introductions of outbreak strains into Puerto Rico, Honduras, Colombia, other Caribbean islands, and the continental United States. We find that ZIKV circulated undetected in multiple regions for many months before the first locally transmitted cases were confirmed, highlighting the importance of surveillance of viral infections. We identify mutations with possible functional implications for ZIKV biology and pathogenesis, as well as those that might be relevant to the effectiveness of diagnostic tests

Avaliação da prevalência de mutações transmitidas de resistência aos antirretrovirais e da história evolutiva de clados raros do HIV-1 no Rio de Janeiro em uma população de gestantes antes do início da terapia para prevenção da transmissão vertical

Submitted by Gilvan Almeida ([email protected]) on 2016-11-29T12:56:09Z No. of bitstreams: 1 license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5)Approved for entry into archive by Anderson Silva ([email protected]) on 2017-02-10T12:50:03Z (GMT) No. of bitstreams: 2 edson_delatorre_ioc_dout_2015.pdf: 25957937 bytes, checksum: facc2f7807ee52355e4dad3434708926 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5)Made available in DSpace on 2017-02-10T12:50:03Z (GMT). No. of bitstreams: 2 edson_delatorre_ioc_dout_2015.pdf: 25957937 bytes, checksum: facc2f7807ee52355e4dad3434708926 (MD5) license.txt: 1748 bytes, checksum: 8a4605be74aa9ea9d79846c1fba20a33 (MD5) Previous issue date: 2015Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, BrasilA epidemia global do HIV está evoluindo em direção à um aumento nas taxas de mutações de resistência e diversidade molecular. Estudos prévios conduzidos na região metropolitana do estado do Rio de Janeiro (RJ) encontraram prevalências moderadas de mutações transmitidas de resistência às drogas antirretrovirais (MTRD) do HIV-1 e uma alta diversidade molecular. Neste trabalho, avaliamos a prevalência das MTRD e a história evolutiva de clados raros do HIV-1 no RJ em uma população de gestantes virgens de terapia. Foram observadas mudanças na tendência das MTRD com as maiores taxas (de inibidores nucleosídicos da transcriptase reversa para inibidores da protease) e um aumento na prevalência de subtipos não-B quando comparados a um estudo anterior conduzido no mesmo local cinco anos antes. As MTRD encontradas podem afetar o desfecho virológico dos regimes antirretrovirais padrão adotados para prevenção da transmissão vertical do HIV-1. Além disso, o nível de MTRD encontrado nesta população de gestantes é considerado alto e justifica a importância da realização da genotipagem prétratamento do HIV para determinação de resistência. Através das análises evolutivas dos clados do HIV-1 raramente encontrados no RJ, verificou-se a circulação de linhagens do subtipo C, CRF02_AG e CRF45_cpx provavelmente importadas do continente africano. A maioria das sequências brasileiras do subtipo C formaram um clado monofilético, que provavelmente se originou no Burundi e foi introduzido no estado do Paraná por volta de 1975, disseminando-se rapidamente para outras regiões brasileiras, incluindo o RJ Cinco introduções adicionais de cepas do subtipo C provavelmente originadas em países da África Oriental, Meridional e Central foram detectadas no estado do RJ. As sequências brasileiras do CRF02_AG distribuíramse em cinco linhagens distintas, provavelmente originadas na África Ocidental, provavelmente Gana, Senegal e Nigéria. Dois clados monofiléticos compostos somente por sequências fluminenses foram identificados, com datas de origem estimadas por volta de 1985. Dentre as 10 amostras recombinantes com fragmentos do subtipo K do HIV-1 isoladas no RJ e que tiveram seus genomas parciais ou quase totais sequenciados, seis mostraram um padrão similar ao CRF45_cpx ao longo de todo o genoma. As restantes foram classificadas como recombinantes de segunda-geração entre o CRF45_cpx e os subtipos B e F1, prevalentes na epidemia brasileira. Todas as sequências CRF45_cpx brasileiras, exceto uma, formaram um clado monofilético, que parece ser o resultado de um único evento de introdução ocorrido por volta de 1984. Esta linhagem se disseminou pelos estados do RJ, São Paulo e Minas Gerais e é relacionada a sequências da Argentina, Itália e Bélgica. Estas análises filogenéticas indicam um influxo contínuo de linhagens do HIV-1 de origem africana no Brasil, que foram introduzidas e/ou tem se disseminado no RJ nos últimos 30-40 anos, demonstrando a importância deste estado para a introdução de novas variantes do HIV na epidemia brasileiraAbstract: The global HIV epidemic is evolving towards an increase in the rates of resistance mutations and molecular diversity. Previous studies conducted in the metropolitan region of Rio de Janeiro (RJ) state have found moderate prevalences of transmitted drug resistance mutations (TDRM) and high molecular diversity of HIV-1. In this work, we evaluated the prevalence of TDRM and the evolutionary history of rare HIV-1 clades in RJ found in an antiretroviral-naive pregnant women population. A change in the trend of the TDRM with higher rates (from nucleoside reverse transcriptase inhibitors to protease inhibitors) and an increase in the prevalence of non-B subtypes were observed when compared to a previous study conducted at the same location five years earlier. The TDRM level found in this population can affect the virological outcome of standard antiretroviral regimens to prevent HIV-1 vertical transmission. The TDRM level found in this pregnant women population is considered high and reinforce the relevance of the pretreatment genotyping of HIV for resistance determination. Through evolutionary analysis of HIV-1 clades rarely found in RJ, the circulation of HIV lineages of subtype C, CRF02_AG and CRF45_cpx probably imported from Africa were observed. Most Brazilian sequences of subtype C branched into a single monophyletic clade, which probably originated in Burundi and was introduced in Paraná state around 1975, spreading rapidly to other regions, including RJ. Five additional introductions of subtype C strains probably originated in Eastern, Central and Southern African countries were detected in the RJ. The Brazilian CRF02_AG sequences were distributed in five distinct lineages, which probably originated in West Africa, probably Ghana, Senegal and Nigeria Two monophyletic clades formed only by sequences from RJ were identified, and their origin dates were estimated at around 1985. Among the 10 samples with HIV-1 subtype K recombinant fragments isolated in RJ who had their partial or near-full length genomes sequenced, six showed a CRF45_cpx-like pattern throughout the genome. The remaining ones were classified as second-generation recombinants between CRF45_cpx and subtypes B and F1, prevalent in the Brazilian epidemic. All Brazilian CRF45_cpx sequences, except one, formed a monophyletic clade that seems to be the result of a single introduction event occurred around 1984. This lineage has spread through the states of RJ, São Paulo and Minas Gerais and is related to sequences from Argentina, Italy and Belgium. These phylogenetic analyzes indicate a continuous influx of HIV-1 African strains in Brazil, which were introduced and/or has spread in Rio de Janeiro in the last 30-40 years, demonstrating the importance of this state to the introduction of new HIV variants in the Brazilian epidemi

Investigating the Role of Easter Island in Migration of Zika Virus from South Pacific to Americas

The role of Easter Island in the dissemination of Zika virus from the Pacific islands into the Americas remains unclear. We analyzed new Zika virus sequences from Eastern Island and found that Zika virus was independently disseminated from French Polynesia into the Americas and Easter Island at around the same time