A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support.

Journal: Retrovirology
PMID: 27998283

Abstract

BACKGROUND: CCR5-coreceptor antagonists can be used for treating HIV-2 infected individuals. Before initiating treatment with coreceptor antagonists, viral coreceptor usage should be determined to ensure that the virus can use only the CCR5 coreceptor (R5) and cannot evade the drug by using the CXCR4 coreceptor (X4-capable). However, until now, no online tool for the genotypic identification of HIV-2 coreceptor usage had been available. Furthermore, there is a lack of knowledge on the determinants of HIV-2 coreceptor usage. Therefore, we developed a data-driven web service for the prediction of HIV-2 coreceptor usage from the V3 loop of the HIV-2 glycoprotein and used the tool to identify novel discriminatory features of X4-capable variants.

Authors

  • Matthias Döring
    Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Campus E 1 4, 66123, Saarbrücken, Germany. mdoering@mpi-inf.mpg.de.
  • Pedro Borrego
    Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal.
  • Joachim Büch
    Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Campus E 1 4, 66123, Saarbrücken, Germany.
  • Andreia Martins
    Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal.
  • Georg Friedrich
    Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Campus E 1 4, 66123, Saarbrücken, Germany.
  • Ricardo Jorge Camacho
    Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven-University of Leuven, Minderbroedersstraat 10, 3000, Louvain, Belgium.
  • Josef Eberle
    Department of Virology, Max von Pettenkofer-Institut, Ludwig-Maximilians-University, Pettenkoferstraße 9a, 80336, Munich, Germany.
  • Rolf Kaiser
    Institute for Virology, University of Cologne, Fürst-Pückler-Str. 56, 50935, Cologne, Germany.
  • Thomas Lengauer
    Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, 66123, Germany.
  • Nuno Taveira
    Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Av. Professor Gama Pinto, 1649-003, Lisbon, Portugal.
  • Nico Pfeifer
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken and Saarbrücken Graduate School of Computer Science, Saarland University, 66123 Saarbrücken.

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