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Armenia D, Spagnuolo V, Bellocchi MC, Galli L, Duca L, Marchegiani G, Clemente T, Carioti L, Lolatto R, Calza L, Celesia BM, Cascio A, Francisci D, Saracino A, Torti C, Zazzi M, Castagna A, Santoro MM. Use of next-generation sequencing on HIV-1 DNA to assess archived resistance in highly treatment-experienced people with multidrug-resistant HIV under virological control: data from the PRESTIGIO Registry. J Antimicrob Chemother 2024:dkae236. [PMID: 39004997 DOI: 10.1093/jac/dkae236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/22/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND To clarify whether next-generation sequencing (NGS) can be useful for resistance assessment in virologically suppressed highly treatment-experienced (HTE) individuals with MDR HIV. METHODS Ninety-one participants from the PRESTIGIO Registry were included. NGS was performed on HIV-DNA at 1%, 5% and 20% cut-offs; major drug resistance mutations (DRMs) were evaluated and compared with those detected in historical plasma genotypic resistance testing (h-GRT). APOBEC editing was also characterized. RESULTS Participants had a complex and long treatment history [median 23 (IQR 21-25) years of ART exposure) and had been virologically suppressed since a median of 3 (IQR 2-5) years. Among all major DRMs detected by HIV-DNA NGS and/or h-GRT, 30% were exclusively found through NGS. The highest detection rate of historical major DRMs was reached with NGS set at 1%, but unusual substitutions and extensive APOBEC hypermutations suggest technical issues and poor clinical relevance in the 1%-5% interval. At NGS set at 5%, 67.2% of historical major DRMs were detected. The number of major DRMs detected exclusively by DNA-NGS as minority variants (frequency 5%-20%) was significantly higher in individuals who later experienced virological rebound compared with those who maintained virological control [median 2 (IQR 1-3) versus 1 (0-2), P = 0.030] and positively correlated with viraemia levels at rebound (rho = 0.474, P = 0.030). CONCLUSIONS In non-viraemic people with an MDR virus, HIV-1 DNA NGS set at 5% is an acceptable technical cut-off that might help to reveal mutations with a potential clinical relevance. Moreover, the number of minority resistance mutations additionally detected by NGS might be associated with loss of virological control.
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Affiliation(s)
- Daniele Armenia
- Departmental Faculty, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Vincenzo Spagnuolo
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Maria C Bellocchi
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Laura Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Greta Marchegiani
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Tommaso Clemente
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
| | - Riccardo Lolatto
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
| | - Leonardo Calza
- Department of Medical and Surgical Sciences, Unit of Infectious Diseases, Policlinico Sant'Orsola-Malpighi, Bologna, Italy
| | | | - Antonio Cascio
- Infectious and Tropical Diseases Unit-Department of Health Promotion, Maternal and Infant Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Daniela Francisci
- Clinic of Infectious Diseases, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | | | - Carlo Torti
- Dipartimento di Scienze di Mediche e Chirurgiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milan, Italy
- Faculty of Medicine and Surgery, Vita-Salute San Raffaele University, Milan, Italy
| | - Maria M Santoro
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
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Andre-Garnier E, Bocket L, Bourlet T, Hocqueloux L, Lepiller Q, Maillard A, Reigadas S, Barriere G, Durand F, Montes B, Stefic K, Marcelin AG. Use of genotypic HIV DNA testing: a DELPHI-type consensus. J Antimicrob Chemother 2024; 79:578-588. [PMID: 38269616 PMCID: PMC10904721 DOI: 10.1093/jac/dkae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES As many disparities in the clinical use of HIV DNA sequencing are observed, a DELPHI-type consensus was initiated in France to homogenize use, techniques and interpretation of results. METHODS Based on a literature review and clinical experience, a steering committee (SC) of eight virologists and one infectious disease specialist formulated statements. Statements were submitted to an independent and anonymous electronic vote of virologists and HIV clinicians in France, between October 2022 and December 2022. RESULTS The SC developed 20 statements grouped into six categories: clinical situations for the use of HIV DNA genotyping; techniques for performing HIV DNA genotyping; consideration of apolipoprotein B mRNA editing enzyme (APOBEC) mutations; genotyping results reporting; recycling of antiretrovirals; and availability of HIV DNA genotyping tests and delays. Twenty-one virologists and 47 clinicians participated in two voting rounds and 18/20 (90%) assertions reached a 'strong' consensus. For example, that prior genotyping on HIV DNA is useful for clinical decision-making when considering switching to some long-acting regimens or to reduce the number of antiretroviral agents in virologically suppressed patients for whom RNA data are unavailable/not exploitable/not sufficiently informative. Two statements achieved no consensus: reporting any detected viral minority population for discussion in multidisciplinary meetings (virologists), and possible risk of virological failure when using a second-generation InSTI plus lamivudine or emtricitabine regimen in patients with undetectable viral load within ≥1 year and in the presence of a documented M184V mutation within the last 5 years (clinicians). CONCLUSIONS This DELPHI-type consensus will facilitate the strengthening and harmonization of good practice when performing HIV DNA sequencing.
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Affiliation(s)
| | - Laurence Bocket
- Virology Department, University Hospital Lille, Lille, France
| | - Thomas Bourlet
- Infectious Agents and Hygiene Department, University Hospital of Saint Etienne, Saint-Etienne, France
| | - Laurent Hocqueloux
- Infectious and Tropical Diseases Department, University Hospital Orléans, Orléans, France
| | - Quentin Lepiller
- Virology Department, University Hospital Besançon, Besançon, France
| | - Anne Maillard
- Virology Department, University Hospital Rennes, Rennes, France
| | | | | | | | - Brigitte Montes
- Virology Department, University Hospital Montpellier, Montpellier, France
| | - Karl Stefic
- Bacteriology, Virology and Hospital Hygene Department, University of Tours, INSERM U1259 MAVIVH, University Hospital Tours, Tours, France
| | - Anne-Geneviève Marcelin
- Virology Departement, Sorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, AP-HP, University Hospitals Pitié-Salpêtrière—Charles Foix, 83, Boulevard de l’hôpital, Paris 75013, France
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3
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Colson P, Bader W, Fantini J, Dudouet P, Levasseur A, Pontarotti P, Devaux C, Raoult D. From viral democratic genomes to viral wild bunch of quasispecies. J Med Virol 2023; 95:e29209. [PMID: 37937701 DOI: 10.1002/jmv.29209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/05/2023] [Accepted: 10/19/2023] [Indexed: 11/09/2023]
Abstract
The tremendous majority of RNA genomes from pathogenic viruses analyzed and deposited in databases are consensus or "democratic" genomes. They represent the genomes most frequently found in the clinical samples of patients but do not account for the huge genetic diversity of coexisting genomes, which is better described as quasispecies. A viral quasispecies is defined as the dynamic distribution of nonidentical but closely related mutants, variants, recombinant, or reassortant viral genomes. Viral quasispecies have collective behavior and dynamics and are the subject of internal interactions that comprise interference, complementation, or cooperation. In the setting of SARS-CoV-2 infection, intrahost SARS-CoV-2 genetic diversity was recently notably reported for immunocompromised, chronically infected patients, for patients treated with monoclonal antibodies targeting the viral spike protein, and for different body compartments of a single patient. A question that deserves attention is whether such diversity is generated postinfection from a clonal genome in response to selection pressure or is already present at the time of infection as a quasispecies. In the present review, we summarize the data supporting that hosts are infected by a "wild bunch" of viruses rather than by multiple virions sharing the same genome. Each virion in the "wild bunch" may have different virulence and tissue tropisms. As the number of viruses replicated during host infections is huge, a viral quasispecies at any time of infection is wide and is also influenced by host-specific selection pressure after infection, which accounts for the difficulty in deciphering and predicting the appearance of more fit variants and the evolution of epidemics of novel RNA viruses.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S 1072, Aix-Marseille Université, Marseille, France
| | - Pierre Dudouet
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille Université., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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Zheng S, Lutters B, Verduyn Lunel F. Sequencing before prescription for immunosuppressed patients. Lancet 2023; 402:1526. [PMID: 37898528 DOI: 10.1016/s0140-6736(23)01133-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/31/2023] [Indexed: 10/30/2023]
Affiliation(s)
- Shuxuan Zheng
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands.
| | - Bart Lutters
- Department of Bioethics and Health Humanities, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
| | - Frans Verduyn Lunel
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht 3584 CX, Netherlands
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