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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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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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High efficacy of switching to bictegravir/emtricitabine/tenofovir alafenamide in people with suppressed HIV and preexisting M184V/I. AIDS 2022; 36:1511-1520. [PMID: 35466963 PMCID: PMC9451915 DOI: 10.1097/qad.0000000000003244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE We investigated the prevalence of preexisting M184V/I and associated risk factors among clinical trial participants with suppressed HIV and evaluated the impact of M184V/I on virologic response after switching to bictegravir/emtricitabine/tenofovir alafenamide (B/F/TAF). DESIGN Participant data were pooled from six clinical trials investigating the safety and efficacy of switching to B/F/TAF in virologically suppressed people with HIV. METHODS Preexisting drug resistance was assessed by historical genotypes and/or baseline proviral DNA genotyping. Virologic outcomes were determined by last available on-treatment HIV-1 RNA. Stepwise selection identified potential risk factors for M184V/I in a multivariate logistic regression model. RESULTS Altogether, 2034 participants switched treatment regimens to B/F/TAF and had follow-up HIV-1 RNA data, and 1825 of these participants had baseline genotypic data available. Preexisting M184V/I was identified in 182 (10%), mostly by baseline proviral DNA genotype ( n = 167). Most substitutions were M184V ( n = 161) or M184V/I mixtures ( n = 10). Other resistance substitutions were often detected in addition to M184V/I ( n = 147). At last on-treatment visit, 98% (179/182) with preexisting M184V/I and 99% (2012/2034) of all B/F/TAF-treated participants had HIV-1 RNA less than 50 copies/ml, with no treatment-emergent resistance to B/F/TAF. Among adult participants, factors associated with preexisting M184V/I included other resistance, black race, Hispanic/Latinx ethnicity, lower baseline CD4 + cell count, advanced HIV disease, longer duration of antiretroviral therapy, and greater number of prior third agents. CONCLUSION M184V/I was detected in 10% of virologically suppressed clinical trial participants at study baseline. Switching to B/F/TAF demonstrated durable efficacy in maintaining viral suppression, including in those with preexisting M184V/I.
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Geretti AM, Blanco JL, Marcelin AG, Perno CF, Stellbrink HJ, Turner D, Zengin T. HIV DNA Sequencing to Detect Archived Antiretroviral Drug Resistance. Infect Dis Ther 2022; 11:1793-1803. [PMID: 35915392 DOI: 10.1007/s40121-022-00676-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Proviral HIV DNA integrated within CD4 T-cells maintains an archive of viral variants that replicate during the course of the infection, including variants with reduced drug susceptibility. We considered studies that investigated archived drug resistance, with a focus on virologically suppressed patients and highlighted interpretative caveats and gaps in knowledge. RESULTS Either Sanger or deep sequencing can be used to investigate resistance-associated mutations (RAMs) in HIV DNA recovered from peripheral blood. Neither technique is free of limitations. Furthermore, evidence regarding the establishment, maintenance, expression and clinical significance of archived drug-resistant variants is conflicting. This in part reflects the complexity of the HIV proviral landscape and its dynamics during therapy. Clinically, detection of RAMs in cellular HIV DNA has a variable impact on treatment outcomes, modulated by the drugs affected, treatment duration and additional determinants of virological failure, including those leading to suboptimal drug exposure. CONCLUSIONS Sequencing cellular HIV DNA can provide helpful complementary information in treatment-experienced patients with suppressed plasma HIV RNA who require a change of regimen. However, care should be taken when interpreting the results. Presence of RAMs is not necessarily a barrier to treatment success. Conversely, even the most sensitive sequencing techniques will fail to provide a comprehensive view of the HIV DNA archive. To inform treatment decisions appropriately, the overall clinical and treatment history of a patient must always be considered alongside the results of resistance testing. Prospective controlled studies are needed to validate the utility of drug resistance testing using cellular HIV DNA.
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Affiliation(s)
- Anna Maria Geretti
- Department of Infectious Diseases, Fondazione PTV and University of Rome Tor Vergata, Viale Oxford 81, 00133, Rome, Italy. .,School of Immunology & Microbial Sciences, King's College London, London, UK.
| | - Jose Luis Blanco
- Infectious Diseases Department, Hospital Clinic of Barcelona, Barcelona, Spain.,Infectious Diseases & AIDS Unit Hospital Clinic Barcelona, University of Barcelona, Barcelona, Spain
| | - Anne Genevieve Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpital Pitié-Salpêtrière, Virologie, 75013, Paris, France
| | - Carlo Federico Perno
- Multimodal Medicine Research Area, Children Hospital IRCCS Bambino Gesù, Rome, Italy
| | | | - Dan Turner
- Crusaid Kobler AIDS Center, Tel Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tuba Zengin
- Global Medical Affairs HIV, Gilead Sciences, London, UK
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Abstract
PURPOSE OF REVIEW HIV-1 drug resistance (HIV DR) testing is routinely performed by genotyping plasma viruses using Sanger population sequencing. Next-generation sequencing (NGS) is increasingly replacing standardized Sanger sequencing. This opens up new opportunities, but also brings challenges. RECENT FINDINGS The number of NGS applications and protocols for HIV DR testing is increasing. All of them are noninferior to Sanger sequencing when comparing NGS-derived consensus sequences to Sanger sequencing-derived sequences. In addition, NGS enables high-throughput sequencing of near full-length HIV-1 genomes and detection of low-abundance drug-resistant HIV-1 variants, although their clinical implications need further investigation. Several groups have defined remaining challenges in implementing NGS protocols for HIV-1 resistance testing. Some of them are already being addressed. One of the most important needs is quality management and consequently, if possible, standardization. SUMMARY The use of NGS technologies on HIV DR testing will allow unprecedented insights into genomic structures of virus populations that may be of immediate relevance to both clinical and research areas such as personalized antiretroviral treatment. Efforts continue to tackle the remaining challenges in NGS-based HIV DR testing.
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The future of long-acting cabotegravir plus rilpivirine therapy: Deeds and misconceptions. Int J Antimicrob Agents 2022; 60:106627. [PMID: 35760225 DOI: 10.1016/j.ijantimicag.2022.106627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/13/2022] [Accepted: 06/19/2022] [Indexed: 11/23/2022]
Abstract
HIV infection is currently managed as a chronic disease thanks to the improvement of antiretroviral therapy (ART). In this light, treatment is lifelong. Therefore, switch to new regimens is a natural event during long-term therapies to avoid problems related to toxicity, adherence, failure and potential selection of drug resistance. In this context, coformulations of multiple agents in one pill and the development of novel drug classes and drugs with high genetic barrier to resistance are now available. The recent approval of the long-acting once monthly or bimonthly injectable combination of the second-generation strand transfer integrase inhibitor (InSTI) cabotegravir (CAB) together with the non-nucleoside reverse transcriptase inhibitor (NNRTI) rilpivirine (RPV) represents the most recent achievement along the line of potent and convenient ART. Several pivotal trials (such as LATTE-2, ATLAS, FLAIR, and ATLAS-2M) largely demonstrated the high efficacy and safety of this long-acting formulation used as an induction-maintenance strategy. Few confirmed virological failures (CVF) have been observed. The combination of at least two baseline factors among HIV-1 subtype A6/A1, a body mass index ≥30 kg/m2, and RPV resistance associated mutations, was associated with an increased risk of CVF at week 48. Available data indicate that this long-acting therapeutic strategy is attractive and potent, thus defining the most appropriate patient and how to handle practical issues is warranted.
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