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Mchantaf G, Cheret A, Melard A, Essat A, Gardiennet E, Bauer R, Charre C, Meiffredy V, Piroth L, Goujard C, Meyer L, Avettand-Fenoel V. The build-up of stock of stable integrated proviruses overtime explains the difficulty in reducing HIV-1 DNA levels when treatment is initiated at the chronic stage of the infection. J Virus Erad 2023; 9:100357. [PMID: 38188640 PMCID: PMC10770741 DOI: 10.1016/j.jve.2023.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Background Understanding factors affecting the size and the evolution of the HIV reservoir is essential for the development of curative strategies. This study aimed to assess the impact of antiretroviral therapy (ART) initiated during primary infection (PHI) vs chronic infection (CHI) on the levels and dynamics of integrated HIV-1 DNA, a biomarker of viral persistence. Methods Integrated and total HIV-1-DNA were measured in the blood of 92 patients treated during PHI (early group) and 41 during CHI (deferred group), at diagnosis, ART initiation, and 12-24 months on treatment. Results On ART, detectable (>1.78 log10 copies/106 PBMCs) integrated HIV-1 DNA levels were significantly lower in the early vs deferred group (2.99 log10vs 3.29 log10,p = 0.005). The proportion of undetectable integrated HIV-1 DNA tended to be higher in the early group vs deferred group (61 % vs 46 %; p = 0.133). Conclusion Treatment initiated at PHI limits the levels of integrated HIV-1 DNA in blood. However, initiating treatment at CHI does not allow reaching such low levels in most patients, probably because the stable proviruses at that stage are present in the less prone to elimination long-lived cells. Thus, early ART could provide an opportunity to preparing for functional cure and eradication strategies.
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Affiliation(s)
- Gilbert Mchantaf
- CHU d’Orléans, Orléans, France
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
- Université d’Orléans, Orléans, France
| | - Antoine Cheret
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
- Plateforme de Médecine Ambulatoire, CHU Guadeloupe, France
| | - Adeline Melard
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
| | - Asma Essat
- Centre de Recherche en Epidémiologie et Santé des Populations (CESP), INSERM U1018, Université Paris Saclay, Le Kremlin-Bicêtre, France
- AP-HP, Service d’Epidémiologie et de Santé Publique, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Elise Gardiennet
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
| | | | - Caroline Charre
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
- AP-HP, Laboratoire de Virologie, Hôpital Cochin, Paris, France
| | | | - Lionel Piroth
- Infectious Diseases Department, Dijon University Hospital, INSERM CIC 1432, Module Épidémiologie Clinique, Université de Bourgogne, Dijon, France
| | - Cécile Goujard
- Centre de Recherche en Epidémiologie et Santé des Populations (CESP), INSERM U1018, Université Paris Saclay, Le Kremlin-Bicêtre, France
- AP-HP, Service de Médecine Interne et d’Immunologie Clinique, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Laurence Meyer
- Centre de Recherche en Epidémiologie et Santé des Populations (CESP), INSERM U1018, Université Paris Saclay, Le Kremlin-Bicêtre, France
- INSERM SC10-US19, Villejuif, France
- AP-HP, Service d’Epidémiologie et de Santé Publique, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Véronique Avettand-Fenoel
- CHU d’Orléans, Orléans, France
- INSERM U1016, CNRS UMR8104, Université Paris Cité, Institut Cochin, Paris, France
- Université d’Orléans, Orléans, France
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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Powell L, Dhummakupt A, Siems L, Singh D, Le Duff Y, Uprety P, Jennings C, Szewczyk J, Chen Y, Nastouli E, Persaud D. Clinical validation of a quantitative HIV-1 DNA droplet digital PCR assay: Applications for detecting occult HIV-1 infection and monitoring cell-associated HIV-1 dynamics across different subtypes in HIV-1 prevention and cure trials. J Clin Virol 2021; 139:104822. [PMID: 33930698 PMCID: PMC8212401 DOI: 10.1016/j.jcv.2021.104822] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/06/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND In HIV-1-exposed infants, nucleic acid testing (NAT) is required to diagnose infection since passively transferred maternal antibodies preclude antibody testing. The sensitivity of clinical NAT assays is lowered with infant antiretroviral prophylaxis and, with empiric very early antiretroviral treatment of high-risk infants, thereby impacting early infant diagnosis. Similarly, adult HIV-1 infections acquired under pre-exposure prophylaxis may occur at low levels, with undetectable plasma viremia and indeterminate antibody tests, for which HIV-1 DNA testing maybe a useful adjunct. Cell-associated HIV-1 DNA concentrations are also used to monitor HIV-1 persistence in viral reservoirs with relevance to HIV-1 cure therapeutics, particularly in perinatal infections. OBJECTIVES We clinically validated an HIV-1 DNA quantitative assay using droplet digital PCR (ddPCR), across different HIV-1 subtypes. STUDY DESIGN The analytical sensitivity and specificity of an HIV-1 DNA ddPCR assay was determined using serial dilutions of a plasmid containing HIV-1 LTR-gag spiked into peripheral blood mononuclear cells (PBMCs), with MOLT-4 cells or PBMCs infected with different HIV-1 subtypes (A, B and C), and U1 cells spiked into PBMCs. Inter- and intra-run variability were used to determine assay precision. RESULTS The HIV-1 LTR-gag ddPCR assay was reliable and reproducible, and exhibited high analytical specificity with sensitivity to near single copy level, across multiple HIV-1 subtypes, and a limit of detection of 4.09 copies/million PBMCs. CONCLUSIONS This assay has applications for detecting occult HIV-1-infection in the setting of combination and long-acting regimens used for HIV-1 prevention, across different HIV-1 subtypes, in infants and adults, and in HIV-1 cure interventions.
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Affiliation(s)
- Laura Powell
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Adit Dhummakupt
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Lilly Siems
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Dolly Singh
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Yann Le Duff
- Center for AIDS Reagents, National Institute for Biological Standards and Controls, England, UK
| | - Priyanka Uprety
- Department of Pathology and Laboratory Medicine, Robert Wood Johnson University Hospital, Rutgers University, New Brunswick, NJ, United States
| | - Cheryl Jennings
- Rush University Medical Center, Department of Molecular Pathogens and Immunity, Chicago, IL, United States
| | - Joseph Szewczyk
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Ya Chen
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States
| | - Eleni Nastouli
- Department of Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health and Francis Crick Institute, London, UK
| | - Deborah Persaud
- Johns Hopkins University, School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Baltimore, MD, United States; Departments of Molecular Microbiology and Immunology and International Health, Johns Hopkins Bloomberg School of Public Health, United States.
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