title: Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing.
abstract: OBJECTIVE
  Resistant minority variants present before ART can be a source of virological failure. This has been shown for NRTIs, NNRTIs and CCR5 inhibitors. However, very few data are available for the detection of such minority resistant variants that could be selected at virological failure and not detected using classical Sanger sequencing.
  
  
  METHODS
  We studied 26 patients treated with tenofovir, emtricitabine and efavirenz with their first virological failure (defined as two consecutive viral loads >50 copies/mL). We performed standard Sanger sequencing and ultradeep sequencing (UDS; Roche 454(®) Life Sciences) in plasma at failure. For UDS, mutations >1% were considered. We compared the presence of reverse transcriptase mutations between the two techniques, using the latest ANRS algorithm.
  
  
  RESULTS
  UDS detected more resistance mutations in 38.5% of cases (10/26 patients) and the genotypic sensitivity score (GSS) was reduced for 6 of them (23.1%). The GSS was impacted more often for NRTIs than for NNRTIs, for which most mutations were already detected by Sanger sequencing. Resistant minority variants were detected even in patients with low viral load at failure.
  
  
  CONCLUSIONS
  These results strongly argue for the use of next-generation sequencing in patients failing on an NRTI+NNRTI regimen, as UDS has the potential to modify the choice of the subsequent regimen.
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France eve.todesco@psl.aphp.fr.
authors.forename: Eve
authors.initials: E
authors.lastname: Todesco
authors.affiliation: Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France INSERM U955, Créteil, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Rodriguez
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Saint Antoine, AP-HP Paris, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Morand-Joubert
authors.affiliation: Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Mercier-Darty
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Desire
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Wirden
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Saint Antoine, AP-HP Paris, France.
authors.forename: Pierre-Marie
authors.initials: PM
authors.lastname: Girard
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP Paris, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Katlama
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Calvez
authors.affiliation: Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France.
authors.forename: Anne-Geneviève
authors.initials: AG
authors.lastname: Marcelin
mesh_terms: D000480:Alkynes; D019380:Anti-HIV Agents / Q000494:pharmacology*; D048588:Benzoxazines / Q000494:pharmacology*; D003521:Cyclopropanes; D024882:Drug Resistance, Viral; D000068679:Emtricitabine / Q000494:pharmacology*; D060005:Genotyping Techniques / Q000379:methods; D006678:HIV / Q000187:drug effects* / Q000235:genetics; D015658:HIV Infections / Q000188:drug therapy; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008826:Microbial Sensitivity Tests / Q000379:methods*; D010949:Plasma / Q000821:virology; D000068698:Tenofovir / Q000494:pharmacology*; D017211:Treatment Failure
chemical_list: D000480:Alkynes; D019380:Anti-HIV Agents; D048588:Benzoxazines; D003521:Cyclopropanes; D000068698:Tenofovir; D000068679:Emtricitabine; C098320:efavirenz
keywords: HIV-1 drug resistance; minority variants; resistance genotyping; virological failure