Misidentification of a Hepatitis C Virus (HCV) recombinant form leading to treatment failure with new direct acting antivirals

International audienc

Evolution of HIV-1 groups M and O: genetic comparative analysis of 23 HIV-1/MO inter-group recombinant forms

International audienc

Analyse des régions LTR du génome d'un VIH-1 recombinant inter-groupes M et O : étude de l'émergence des points de cassure et caractérisation des différentes populations

International audienc

Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: Citogenomic characterization of transposable elements and satellite DNA

Background: The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. Results: Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed. Conclusion: P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora

HIV-1/M+O INTERGROUP DUAL INFECTIONS AND ASSOCIATED HIV-MO RECOMBINANTS IN FRANCE FROM 2004 TO 2014

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HIV-1 group P infection: towards a dead-end infection?

HIV/1 group P (HIV-1/P) is the last HIV/1 group discovered and to date, comprises only two strains. To obtain new insights into this divergent group, we screened for new infections by developing specific tools, and analysed phenotypic and genotypic properties of the prototypic strain RBF168. In addition, the follow-up of the unique patient monitored so far, has raised the knowledge of the natural history of this infection and its therapeutic management. We developed an HIV-1/P specific sero-molecular strategy and screened over 29,498 specimen samples. Infectivity and evolution of the gag-30 position, considered as marker of adaptation to human, were explored by successive passages of RBF168 strain onto human PBMCs. Natural history and immuno-virological responses to combined antiretroviral therapy (cART) were analysed based on CD4 counts and plasmatic viral load evolution. No new infection was detected. Infectivity of RBF168 was found lower, relative to other main HIV groups and the conservative methionine found in the gag-30 position revealed a lack of adaptation to human. The follow-up of the patient during the five-year ART-free period, showed a relative stability of CD4 cell count with a mean of 326 mm. Initiation of cART led to rapid RNA undetectability with a significant increase of CD4, reaching 687 mm after 8 years. Our results showed that HIV-1/P strains remain extremely rare and could be less adapted and pathogenic than other HIV strains. These data lead to the hypothesis that HIV-1/P infection could evolve towards, or even already correspond to, a dead-end infection