title: Drug resistance and tropism as markers of the dynamics of HIV-1 DNA quasispecies in blood cells of heavily pretreated patients who achieved sustained virological suppression.
abstract: OBJECTIVE
  The objective of this study was to address the dynamics of archived resistant quasispecies in cell-associated HIV-1 DNA over time in heavily ART-experienced patients with currently suppressed plasma HIV-1 RNA.
  
  
  METHODS
  Longitudinal ultra-deep sequencing (UDS) analysis of reverse transcriptase, protease and V3 Env regions was performed on blood-cell-associated HIV-1 DNA samples. Drug-resistance-associated mutations (DRAMs) and tropism were interpreted using the ANRS and Geno2Pheno algorithms. We analysed frozen blood cells from patients enrolled in the INNOVE and ANRS 123 ETOILE studies who achieved sustained viral suppression after salvage optimized ART (SOT).
  
  
  RESULTS
  Samples were available at baseline and 6 and ≥12 months after SOT initiation in 10 patients. V3 loop sequences displayed wide intra-individual dynamics over time. Viral variants harbouring DRAMs exhibited three non-exclusive scenarios. First, when SOT exerted the same selective pressure as previous failing regimens, some viral quasispecies still harboured the same DRAMs at the same level as at the time of virological failure. Thus, as DRAMs were mostly associated with the same viral variant, variants with a complete resistance pattern remained archived. Second, some viral variants harbouring DRAMs were no longer detected over time when SOT consisted of new antiretroviral classes or had resistance profiles distinct from those of previous failing regimens. Third, variants with new DRAMs associated with SOT emerged in blood cells during follow-up despite sustained virological control.
  
  
  CONCLUSIONS
  Using longitudinal UDS analysis and focusing on DRAMs and tropism as markers, we demonstrated that, despite sustained virological control, archived HIV-1 DNA quasispecies continued to evolve.
authors.affiliation: Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Gantner
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France/Department of Virology, Hôpital Saint-Antoine, APHP, Paris, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Morand-Joubert
authors.affiliation: Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Sueur
authors.affiliation: CMIT, 46 Rue Henri Huchard, 75018 Paris, France.
authors.forename: François
authors.initials: F
authors.lastname: Raffi
authors.affiliation: Univ. Bordeaux, ISPED, Centre INSERM U897- Epidemiologie-Biostatistique, F-33000 Bordeaux, France/INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Fagard
authors.affiliation: APHP, Service des Maladies Infectieuses et Tropicales, Hôpital Saint Louis, Paris, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Lascoux-Combe
authors.affiliation: APHP, Service de Médecine Interne, Hôpital Cochin, Paris, France/Université Paris Descartes, Paris, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Salmon
authors.affiliation: UPMC Univ Paris 06, Centre d'Immunologie et de Maladies Infectieuses (CIMI) UMRS CR7, Persistent Viral Infection (PVI) Team, INSERM U1135, Paris, France/APHP, Virology Laboratory, Tenon Hospital, Paris, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Amiel
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, INSERM, UMR_S 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Service de Virologie, Hôpital Pitié-Salpêtrière, AP-HP, Paris, France.
authors.forename: Sidonie
authors.initials: S
authors.lastname: Lambert-Niclot
authors.affiliation: Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75013 Paris, France/Department of Virology, Hôpital Saint-Antoine, APHP, Paris, France.
authors.forename: Djeneba Bocar
authors.initials: DB
authors.lastname: Fofana
authors.affiliation: Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France APHP, Unité Fonctionnelle de Thérapeutique en Immuno-Infectiologie, Centre Hospitalier Universitaire Hôtel-Dieu, Paris, France.
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Viard
authors.affiliation: Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
authors.forename: Samira
authors.initials: S
authors.lastname: Fafi-Kremer
authors.affiliation: Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France APHP, Laboratoire de Microbiologie Clinique, Centre Hospitalier Universitaire Necker Enfants Malades, Paris, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Rouzioux
authors.affiliation: Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France APHP, Laboratoire de Microbiologie Clinique, Centre Hospitalier Universitaire Necker Enfants Malades, Paris, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Avettand-Fenoel
authors.affiliation: Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France APHP, Unité Fonctionnelle de Thérapeutique en Immuno-Infectiologie, Centre Hospitalier Universitaire Hôtel-Dieu, Paris, France jade.ghosn@aphp.fr.
authors.forename: Jade
authors.initials: J
authors.lastname: Ghosn
mesh_terms: D019380:Anti-HIV Agents / Q000627:therapeutic use*; D001773:Blood Cells / Q000821:virology; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D024882:Drug Resistance, Viral; D005838:Genotype; D015658:HIV Infections / Q000188:drug therapy* / Q000821:virology*; D016333:HIV Protease / Q000235:genetics; D054303:HIV Reverse Transcriptase / Q000235:genetics; D015497:HIV-1 / Q000187:drug effects* / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008137:Longitudinal Studies; D009154:Mutation; D056189:Viral Tropism; D054299:env Gene Products, Human Immunodeficiency Virus / Q000235:genetics
chemical_list: D019380:Anti-HIV Agents; D004279:DNA, Viral; D054299:env Gene Products, Human Immunodeficiency Virus; D054303:HIV Reverse Transcriptase; D016333:HIV Protease