Pierre Gantner1, Laurence Morand-Joubert2, Charlotte Sueur3, François Raffi4, Catherine Fagard5, Caroline Lascoux-Combe6, Dominique Salmon7, Corinne Amiel8, Sidonie Lambert-Niclot9, Djeneba Bocar Fofana2, Jean-Paul Viard10, Samira Fafi-Kremer3, Christine Rouzioux11, Véronique Avettand-Fenoel11, Jade Ghosn12. 1. Université Paris Descartes, EA 7327, Université Paris Descartes PRES Sorbonne Paris-Cité, Paris, France Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France. 2. 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. 3. Laboratoire de Virologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France. 4. CMIT, 46 Rue Henri Huchard, 75018 Paris, France. 5. Univ. Bordeaux, ISPED, Centre INSERM U897- Epidemiologie-Biostatistique, F-33000 Bordeaux, France/INSERM, ISPED, Centre INSERM U897-Epidemiologie-Biostatistique, F-33000 Bordeaux, France. 6. APHP, Service des Maladies Infectieuses et Tropicales, Hôpital Saint Louis, Paris, France. 7. APHP, Service de Médecine Interne, Hôpital Cochin, Paris, France/Université Paris Descartes, Paris, France. 8. 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. 9. 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. 10. 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. 11. 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. 12. 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.
Abstract
OBJECTIVES: 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.
OBJECTIVES: 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: Erkki Lathouwers; Eric Y Wong; Kimberley Brown; Bryan Baugh; Anne Ghys; John Jezorwski; El Ghazi Mohsine; Erika Van Landuyt; Magda Opsomer; Sandra De Meyer Journal: AIDS Res Hum Retroviruses Date: 2019-10-21 Impact factor: 2.205