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Home / Archives for Vandamme AM

Vandamme AM

RegaDB: Community-driven data management and analysis for infectious diseases

  • Autores: Alcantara LCJ, Assel M, Ayouba A, Beheydt G, Boucher C, Camacho RJ, Carvalho AP, Cavaco-Silva J, De Bel A, De Munter P, De Oliveira T, Deforche K, Ferreira F, Grossman Z, Imbrechts S, Kaiser R, Lacor P, Lapadula G, Libin P, Otelea D, Paraschiv S, Peeters M, Ruelle J, Sloot P, Snoeck J, Theys K, Torti C, Van Laethem K, Van Wijngaerden E, Vandamme AM, Wesner S, Zazzi M
  • Ano de Publicação: 2013
  • Journal: Bioinformatics
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/23645815

RegaDB is a free and open source data management and analysis environment for infectious diseases. RegaDB allows clinicians to store, manage and analyse patient data, including viral genetic sequences. Moreover, RegaDB provides researchers with a mechanism to collect data in a uniform format and offers them a canvas to make newly developed bioinformatics tools available to clinicians and virologists through a user friendly interface.
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European Recommendations for the Clinical Use of HIV Drug Resistance Testing: 2011 Update.

  • Autores: Camacho RJ, Ceccherini-Silberstein F, De Luca A, European HIV Drug Resistance Guidelines Panel, Palmisano L, Paraskevis D, Paredes R, Poljak M, Schmit JC, Sönnerborg A, Soriano V, Vandamme AM, Walter H
  • Ano de Publicação: 2011
  • Journal: Aids Reviews
  • Link: https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=19&SID=Y2ytOr2frNCuRlReLtM&page=1&doc=1

The European HIV Drug Resistance Guidelines Panel, established to make recommendations to clinicians and virologists, felt that sufficient new information has become available to warrant an update of its recommendations, explained in both pocket guidelines and this full paper.
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Appearance of a single amino acid insertion at position 33 in HIV type 1 protease under a lopinavir-containing regimen, associated with reduced protease inhibitor susceptibility.

  • Autores: Camacho RJ, Detsika MG, Hatzakis A, Imbrechts S, Lazanas M, Lu L, Magiorkinis E, Magiorkinis G, Molla A, Paraskevis D, Pilot-Matias T, Van Laethem K, Vandamme AM
  • Ano de Publicação: 2011
  • Journal: AIDS Research and Human Retroviruses
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Appearance+of+a+Single+Amino+Acid+Insertion+at+Position+33+in+HIV+Type+1+Protease+Under+a+Lopinavir-Containing+Regimen%2C+Associated+with+Reduced+Protease+Inhibitor+Susceptibility

HIV drug resistance is a multifactorial phenomenon and constitutes a major concern as it results in therapy failure. The aim of this study was to assess the impact of an amino acid insertion identified at position 33 of the protease gene, derived from samples from three patients under lopinavir therapy, on viral fitness and protease inhibitor (PI) resistance.
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Structural modifications induced by specific HIV-1 protease-compensatory mutations have an impact on the virological response to a first-line lopinavir/ritonavir-containing regimen

  • Autores: Alcaro S, Alteri C, Antinori A, Artese A, Beheydt G, Bertoli A, Ceccherini-Silberstein F, Costa G, D’Arminio Monforte A, Girardi E, Gori C, Orchi N, Parrotta L, Perno CF, Santoro MM, Svicher V, Theys K, Vandamme AM
  • Ano de Publicação: 2013
  • Journal: J Antimicrob Chemother
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/23687186

This study evaluates the impact of specific HIV-1 protease-compensatory mutations (wild-type amino acids in non-B subtypes) on virological response to a first-line lopinavir/ritonavir-containing regimen in an HIV-1 subtype B-infected population.
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Cellular HIV-1 DNA levels in drug sensitive strains are equivalent to those in drug resistant strains in newly-diagnosed patients in Europe

  • Autores: Balotta C, Clotet B, Demetriou VL, Grossman Z, Jørgensen LB, Kostrikis LG, Kousiappa I, Lepej SZ, Levy I, Nielsen C, Paraskevis D, Poljak M, Roman F, Ruiz L, Schmidt JC, Van de Vijver DA, Van Laethem K, Vandamme AM, Vercauteren J
  • Ano de Publicação: 2010
  • Journal: PLoS One
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/20544014

BACKGROUND:
HIV-1 genotypic drug resistance is an important threat to the success of antiretroviral therapy and transmitted resistance has reached 9% prevalence in Europe. Studies have demonstrated that HIV-1 DNA load in peripheral blood mononuclear cells (PBMC) have a predictive value for disease progression, independently of CD4 counts and plasma viral load.
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Comparative performance of the REGA subtyping tool version 2 versus version 1

  • Autores: Abecasis AB, Camacho RJ, De Oliveira T, Imbrechts S, Libin P, Vandamme AM, Wang Y
  • Ano de Publicação: 2010
  • Journal: Infection Genetics and Evolution
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Comparative+performance+of+the+REGA+subtyping+tool+version+2+versus+version+1

The REGA HIV-1 subtyping tool is a phylogenetic-based method for subtyping HIV-1 genomic sequences that was published in 2005. The subtyping tool combines phylogenetic approaches with recombination detection methods.
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High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains

  • Autores: de Sousa JD, Lemey P, Müller V, Vandamme AM
  • Ano de Publicação: 2010
  • Journal: PLoS One
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=High+GUD+Incidence+in+the+Early+20(th)+Century+Created+a+Particularly+Permissive+Time+Window+for+the+Origin+and+Initial+Spread+of+Epidemic+HIV+Strains

The processes that permitted a few SIV strains to emerge epidemically as HIV groups remain elusive. Paradigmatic theories propose factors that may have facilitated adaptation to the human host (e.g., unsafe injections), none of which provide a coherent explanation for the timing, geographical origin, and scarcity of epidemic HIV strains.
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High GUD incidence in the early 20 century created a particularly permissive time window for the origin and initial spread of epidemic HIV strains

  • Autores: de Sousa JD, Lemey P, Müller V, Vandamme AM
  • Ano de Publicação: 2010
  • Journal: PLoS One
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=High+GUD+Incidence+in+the+Early+20(th)+Century+Created+a+Particularly+Permissive+Time+Window+for+the+Origin+and+Initial+Spread+of+Epidemic+HIV+Strains

The processes that permitted a few SIV strains to emerge epidemically as HIV groups remain elusive. Paradigmatic theories propose factors that may have facilitated adaptation to the human host (e.g., unsafe injections), none of which provide a coherent explanation for the timing, geographical origin, and scarcity of epidemic HIV strains.
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ALISPORIVIR – A HOST-TARGETING ANTIVIRAL, PROVIDES LOW VIRAL BREAKTHROUGH RATE AND HIGH BARRIER TO RESISTANCE IN HCV GENOTYPE 1 TREATMENT-NAiVE PATIENTS IN THE PHASE IIB ESSENTIAL STUDY.

  • Autores: Avila C, Bao WB, Crabbe R, Jones CT, Li B, Lin K, Naoumov NV, Snoeck J, Tang J, Tiongyip C, Vandamme AM, Vuagniaux G, Yu J
  • Ano de Publicação: 2011
  • Journal: Hepatology
  • Link: https://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=46&SID=2CbhBUDoSw8ZkFBEQLW&page=1&doc=1

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Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients.

  • Autores: Albert J, Åsjö B, Balotta C, Boucher CA, Bruckova M, Camacho RJ, Clotet B, Coughlan S, Deforche K, Grossman Z, Hamouda O, Horban A, Korn K, Kostrikis LG, Kücherer C, Libin P, Liitsola K, Nielsen C, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Riva C, Ruiz L, Schmit JC, Schuurman R, Sönnerborg A, SPREAD-programme, Staneková D, Stanojevic M, Struck D, Theys K, Van de Vijver DA, Van Laethem K, Vandamme AM, Vercauteren J, Wensing AM
  • Ano de Publicação: 2012
  • Journal: Retrovirology
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Treatment-associated+polymorphisms+in+protease+are+significantly+associated+with+higher+viral+load+and+lower+CD4+count+in+newly+diagnosed+drug-naive+HIV-1+infected+patients

BACKGROUND:
The effect of drug resistance transmission on disease progression in the newly infected patient is not well understood. Major drug resistance mutations severely impair viral fitness in a drug free environment, and therefore are expected to revert quickly. Compensatory mutations, often already polymorphic in wild-type viruses, do not tend to revert after transmission.
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