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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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Armenia D, Gagliardini R, Alteri C, Svicher V, Cento V, Borghi V, Vergori A, Cicalini S, Forbici F, Fabeni L, Bertoli A, Brugneti M, Gennari W, Malagnino V, Andreoni M, Mussini C, Antinori A, Perno CF, Santoro MM, Ceccherini-Silberstein F. Temporal trend of drug-resistance and APOBEC editing in PBMC genotypic resistance tests from HIV-1 infected virologically suppressed individuals. J Clin Virol 2023; 168:105551. [PMID: 37573167 DOI: 10.1016/j.jcv.2023.105551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND We aimed at evaluating the temporal trend of drug-resistance and APOBEC editing from HIV-DNA genotypic resistance tests (GRT) in virologically suppressed individuals. MATERIAL AND METHODS Major resistance mutations (MRM), genotypic susceptibility score (GSS) for the current regimen and APOBEC-related mutations (APO-M) were evaluated. Potential changes in trends of MRM and APO-M over-time were assessed and predictors of MRM detection or sub-optimal GSS (GSS<2) at HIV-DNA-GRT were estimated through logistic regression analyses. RESULTS Among the 1126 individuals included, 396 (35.2%) harboured at least one MRM (23.4% to NRTI, 18.8% to NNRTI, 7.7% to PI and 1.4% to INSTI [N=724]); 132 (12.3%) individuals showed a GSS <2. APO-M and stop codons were found in 229 (20.3%) and 105 (9.3%) individuals, respectively. APO-DRMs were found in 16.8% of individuals and were more likely observed in those individuals with stop codons (40.0%) compared to those without (14.4%, P<0.001). From 2010 to 2021 no significant changes of resistance or APO-M were found. Positive predictors of MRM detection at HIV-DNA GRT were drug abuse, subtype B infection, and a prolonged and complex treatment history. Perinatal infection and having at least 2 stop codons were associated with a current suboptimal regimen. CONCLUSIONS In virologically suppressed individuals, resistance in HIV-DNA and the extent of APOBEC editing were generally stable in the last decade. A careful evaluation of APOBEC editing might be helpful to improve the reliability of HIV-DNA GRT. Further investigations are required to understand how to apply the estimation of APOBEC editing in refining genotypic evaluation.
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Affiliation(s)
- D Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - R Gagliardini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - C Alteri
- University of Milan, Milan, Italy
| | - V Svicher
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - V Cento
- Humanitas Research Hospital, IRCCS, Milan, Italy
| | - V Borghi
- University of Modena and Reggio Emilia, Modena, Italy
| | - A Vergori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - S Cicalini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - F Forbici
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - L Fabeni
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - A Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy; Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - M Brugneti
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - W Gennari
- University of Modena and Reggio Emilia, Modena, Italy
| | - V Malagnino
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - M Andreoni
- Polyclinic of Rome "Tor Vergata", Rome, Italy
| | - C Mussini
- University of Modena and Reggio Emilia, Modena, Italy
| | - A Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - C F Perno
- Bambino Gesù Children's Hospital, Rome, Italy
| | - M M Santoro
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
| | - F Ceccherini-Silberstein
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
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Wang R, Wright J, Saggu P, Ait-Khaled M, Moodley R, Parry CM, Lutz T, Podzamczer D, Moore R, Górgolas Hernández-Mora M, Kinder C, Wynne B, van Wyk J, Underwood M. Assessing the Virologic Impact of Archived Resistance in the Dolutegravir/Lamivudine 2-Drug Regimen HIV-1 Switch Study TANGO through Week 144. Viruses 2023; 15:1350. [PMID: 37376649 DOI: 10.3390/v15061350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The TANGO study (ClinicalTrials.gov, NCT03446573) demonstrated that switching to dolutegravir/lamivudine (DTG/3TC) was non-inferior to continuing tenofovir alafenamide-based regimens (TBR) through week 144. Retrospective baseline proviral DNA genotypes were performed for 734 participants (post-hoc analysis) to assess the impact of archived, pre-existing drug resistance on 144-week virologic outcomes by last on-treatment viral load (VL) and Snapshot. A total of 320 (86%) participants on DTG/3TC and 318 (85%) on TBR had both proviral genotype data and ≥1 on-treatment post-baseline VL results and were defined as the proviral DNA resistance analysis population. Archived International AIDS Society-USA major nucleoside reverse transcriptase inhibitor, non-nucleoside reverse transcriptase inhibitor, protease inhibitor, and integrase strand transfer inhibitor resistance-associated mutations (RAMs) were observed in 42 (7%), 90 (14%), 42 (7%), and 11 (2%) participants, respectively, across both groups; 469 (74%) had no major RAMs at baseline. M184V/I (1%), K65N/R (<1%), and thymidine analogue mutations (2%) were infrequent. Through week 144, >99% of participants on DTG/3TC and 99% on TBR were virologically suppressed (last on-treatment VL <50 copies/mL) regardless of the presence of major RAMs. Results from the sensitivity analysis by Snapshot were consistent with the last available on-treatment VL. In TANGO, archived, pre-existing major RAMs did not impact virologic outcomes through week 144.
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Affiliation(s)
- Ruolan Wang
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA
| | | | | | - Mounir Ait-Khaled
- ViiV Healthcare, 980 Great West Road, Brentford TW8 9GS, Middlesex, UK
| | - Riya Moodley
- ViiV Healthcare, 980 Great West Road, Brentford TW8 9GS, Middlesex, UK
| | - Chris M Parry
- ViiV Healthcare, 980 Great West Road, Brentford TW8 9GS, Middlesex, UK
| | - Thomas Lutz
- Infektiologikum, Stresemannallee 3, 60596 Frankfurt am Main, Germany
| | - Daniel Podzamczer
- Hospital Universitari de Bellvitge, Carrer de la Feixa Llarga, s/n, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Moore
- Northside Clinic, 370 St Georges Rd, Fitzroy North, VIC 3068, Australia
| | | | - Clifford Kinder
- AIDS Healthcare Foundation-The Kinder Medical Group, 3661 S Miami Ave Suite 806, Miami, FL 33133, USA
| | - Brian Wynne
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA
| | - Jean van Wyk
- ViiV Healthcare, 980 Great West Road, Brentford TW8 9GS, Middlesex, UK
| | - Mark Underwood
- ViiV Healthcare, 406 Blackwell Street, Suite 300, Durham, NC 27701, USA
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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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Santoro MM, Armenia D, Teyssou E, Santos JR, Charpentier C, Lambert-Niclot S, Antinori A, Katlama C, Descamps D, Perno CF, Calvez V, Paredes R, Ceccherini-Silberstein F, Marcelin AG. Virological efficacy of switch to DTG plus 3TC in a retrospective observational cohort of suppressed HIV-1 patients with or without past M184V: the LAMRES study. J Glob Antimicrob Resist 2022; 31:52-62. [PMID: 35948240 DOI: 10.1016/j.jgar.2022.07.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES The aim of this study was to assess the efficacy of dolutegravir plus lamivudine (DTG+3TC) in a large set of virologically suppressed HIV-1 infected individuals with or without past M184V mutation. METHODS This observational study included individuals who switched to DTG+3TC with ≥1 genotype before switch. Survival analysis was used to evaluate the role of past M184V on virological rebound (VR) or blips after DTG+3TC switch. RESULTS A total of 712 individuals followed in several clinical centres in France, Italy and Spain were analysed. Past M184V was present in 60 (8.4%) individuals. By 3 years after switch, the overall probability of VR and blips was 6.7% and 6.9%, respectively, without any statistical significance according to the presence/absence of past M184V. A significantly higher probability of VR was found in individuals harbouring M184V before DTG+3TC with a duration of virological suppression (Ts) ≤.3.5 years compared to others (M184V+Ts ≤.3.5 years: 22.7%; M184M+Ts ≤.3.5 years: 9.0%; M184V+Ts >3.5 years: 7.8%; M184M+Ts >3.5 years: 4.9%; P = 0.007). This finding was not confirmed in multivariable models adjusting for behavioural and demographic variables. Genotypic resistance test after VR under DTG+3TC was available for 8/39 individuals; one poorly adherent individual developed M184V. No resistance to INIs was found. CONCLUSION In this retrospective observational study, the probability of VR and blips in patients switching to DTG+3TC was very low after 3 years of treatment regardless M184V. The effect of a short duration of previous virological suppression in individuals with M184V remains troubling and needs ad hoc clinical trials to be confirmed.
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Affiliation(s)
| | - Daniele Armenia
- Saint Camillus International University of Health Sciences, Rome, Italy
| | - Elisa Teyssou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - José Ramón Santos
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Charlotte Charpentier
- Service de Virologie, Université de Paris, INSERM, IAME, Hôpital Bichat-Claude Bernard, Paris, France
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Universitaire Saint Antoine, laboratoire de virologie, Paris, France
| | - Andrea Antinori
- Infectious Disease-Clinical Department, National Institute for Infectious Diseases 'L. Spallanzani', IRCCS, Rome, Italy
| | - Christine Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Diane Descamps
- Service de Virologie, Université de Paris, INSERM, IAME, Hôpital Bichat-Claude Bernard, Paris, France
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
| | - Roger Paredes
- Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | - Anne Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, Paris, France
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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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Ji H, Sandstrom P. Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing. Pathogens 2022; 11:pathogens11070739. [PMID: 35889985 PMCID: PMC9321895 DOI: 10.3390/pathogens11070739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
The close monitoring of HIV drug resistance using genotypic HIV drug resistance testing (HIVDRT) has become essential for effective HIV/AIDS management at both individual and population levels. Over the years, a broad spectrum of analytes or specimens have been applied or attempted in HIVDRT; however, the suitability and performance of these analytes in HIVDRT and the clinical relevance of the results from them may vary significantly. This article provides a focused overview of the performance, strengths, and weaknesses of various analytes while used in HIVDRT, which may inform the optimal analytes selection in different application contexts.
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Affiliation(s)
- Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-789-6521
| | - Paul Sandstrom
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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Achieving virological control in pan-resistant HIV-1 infection: A case series. EBioMedicine 2022; 77:103906. [PMID: 35255457 PMCID: PMC8897623 DOI: 10.1016/j.ebiom.2022.103906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/05/2022] Open
Abstract
Background HIV-1 pan-resistance refers to a reduced susceptibility to nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors, protease inhibitors and integrase strand tranfer inhibitors. Although still anecdotal, its management remains a concern both for affected people living with HIV (PLWH) and for public health. Methods We described genotypic resistance testing (GRT) of three PLWH with a documented poor virological response to previous antiretroviral therapies, who started ibalizumab, an anti-CD4 monoclonal antibody, combined with an optimized background therapy. Both historical and most recent GRT on plasma RNA and peripheral blood mononuclear cell DNA were interpreted according to the Stanford HIVDb version 9.0 (last updated on 22 February, 2021). After the switch to a regimen including the monoclonal antibody, HIV-1 RNA has been quantified biweekly (PCR Cobas® HIV-1 test 6800 Systems, Roche Diagnostics). Follow-up was censored at data freezing (16 January, 2021). Findings We report findings from heavily treatment-experienced PLWH with a pan-resistant HIV-1 infection, who achieved virological control once introduced injections of ibalizumab, that is free from cross-resistance with all the antiretroviral drugs available and ensures patient adherence due to a close monitoring attributable to the route of administration, combined with recycled enfuvirtide and an optimized background regimen, selected on the basis of an accurate evaluation of resistance mutations. Interpretation In these cases, this new approach has revealed to be a turning point in achieving virological control. Funding None, this research was supported by internal funding.
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Crespo-Bermejo C, de Arellano ER, Lara-Aguilar V, Valle-Millares D, Gómez-Lus ML, Madrid R, Martín-Carbonero L, Briz V. Persistent low-Level viremia in persons living with HIV undertreatment: An unresolved status. Virulence 2021; 12:2919-2931. [PMID: 34874239 PMCID: PMC8654475 DOI: 10.1080/21505594.2021.2004743] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Antiretroviral therapy (ART) allows suppressed viremia to reach less than 50 copies/mL in most treated persons living with HIV (PLWH). However, the existence of PLWH that show events of persistent low-level viremia (pLLV) between 50 and 1000 copies/mL and with different virological consequences have been observed. PLLV has been associated with higher virological failure (VF), viral genotype resistance, adherence difficulties and AIDS events. Moreover, some reports show that pLLV status can lead to residual immune activation and inflammation, with an increased risk of immunovirological failure and a pro-inflammatory cytokine level which can lead to a higher occurrence of non-AIDS defining events (NADEs) and other adverse clinical outcomes. Until now, however, published data have shown controversial results that hinder understanding of the true cause(s) and origin(s) of this phenomenon. Molecular mechanisms related to viral reservoir size and clonal expansion have been suggested as the possible origin of pLLV. This review aims to assess recent findings to provide a global view of the role of pLLV in PLWH and the impact this status may cause on the clinical progression of these patients.
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Affiliation(s)
- Celia Crespo-Bermejo
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Violeta Lara-Aguilar
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Daniel Valle-Millares
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
| | - Mª Luisa Gómez-Lus
- Departamento de Medicina- Área de Microbiología. Facultad de Medicina. Universidad Complutense, Madrid, Spain
| | - Ricardo Madrid
- Parque Científico de Madrid, Campus de Cantoblanco, Madrid, Spain.,Department of Genetics, Physiology and Microbiology. Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Luz Martín-Carbonero
- Unidad de Vih. Servicio de Medicina Interna. Hospital Universitario La Paz. Instituto de Investigación Sanitaria Hospital de La Paz (Idipaz), Madrid, Spain
| | - Verónica Briz
- Laboratory of Reference and Research on Viral Hepatitis, National Center of Microbiology, Institute of Health Carlos Iii, Majadahonda, Madrid, Spain
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11
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Kao SW, Liu ZH, Wu TS, Ku SWW, Tsai CL, Shie SS, Huang PY, Wu YM, Hsiao YH, Chen NY. Prevalence of drug resistance mutations in HIV-infected individuals with low-level viraemia under combination antiretroviral therapy: an observational study in a tertiary hospital in Northern Taiwan, 2017-19. J Antimicrob Chemother 2021; 76:722-728. [PMID: 33331635 DOI: 10.1093/jac/dkaa510] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/09/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Effective ART is crucial for combating the HIV pandemic. Clinically, plasma viral load monitoring to achieve virological suppression is the guide for an optimal ART. The presence of low-level viraemia (LLV) below the definition level of virological failure is a risk factor for ART failure. However, there is no treatment consensus over LLV yet, mainly due to the limitation of standard HIV-RNA genotyping and the resultant insufficient understanding of LLV characteristics. OBJECTIVES To better profile drug resistance mutations (DRMs) and the associated factors in cases experiencing LLV. METHODS A prospective observational study was conducted from 2017 to 2019. HIV-DNA was used as an alternative to HIV-RNA for HIV genotyping coupled with deep sequencing for ART-naive and ART-failure cases, as well as those with LLV. RESULTS Eighty-one ART-naive, 18 ART-failure and 16 LLV cases received HIV genotyping in the study. Three-quarters (12/16) of cases experiencing LLV harboured DRMs. Cases with LLV had higher prevalence of DRMs to NNRTIs than the ART-naive group (69% versus 20%, P < 0.001), but lower DRM prevalence to NRTIs than the ART-failure group (25% versus 61%, P < 0.001). Approximately half of the LLV cases had issues of suboptimal ART compliance/ART interruption, and 68.8% (11/16) did not display drug resistance to their ART at the time of LLV. CONCLUSIONS HIV DRM profiles in LLV cases were significantly different to those in ART-naive and ART-failure cases. Approaches to consolidate ART compliance and early exploration of potential ART resistance may be needed for cases experiencing LLV episodes.
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Affiliation(s)
- Shu-Wei Kao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Zhuo-Hao Liu
- Department of Neurosurgery, Chang Gung Memorial Hospital, Linkou Branch, Taoyuan, Taiwan
| | - Ting-Shu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Stephane Wen-Wei Ku
- Division of Infectious Diseases, Department of Medicine, Taipei City Hospital Ren-Ai Branch, Taipei, Taiwan.,Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shian-Sen Shie
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Po-Yen Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yen-Mu Wu
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Yu-Hsiang Hsiao
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Nan-Yu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital Linkou Branch, Chang Gung University College of Medicine, Taoyuan, Taiwan
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12
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Soulie C, Assoumou L, Abdi B, Sayon S, Nguyen T, Valantin MA, Beniguel L, Ferre V, Alloui C, Montes B, Avettand-Fenoel V, Delaugerre C, Descamps D, Martinez E, Reynes J, Peytavin G, Costagliola D, Katlama C, Calvez V, Marcelin AG. Characterization of viral rebounds on dual etravirine/raltegravir maintenance therapy (ANRS-163 ETRAL trial). J Antimicrob Chemother 2021; 75:1943-1949. [PMID: 32259255 DOI: 10.1093/jac/dkaa090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The ANRS-163 ETRAL trial, a switch study to an etravirine 200 mg/raltegravir 400 mg twice-daily regimen in 165 patients with HIV-1 infection, showed durable efficacy until Week 96. The aim of this work was to investigate in detail the virological rebounds (VRs), defined as at least one plasma HIV viral load (VL) >50 copies/mL. METHODS Quantification of HIV-DNA level was assessed at baseline, Week 48 and Week 96 (n = 157). VLs were measured in seminal plasma at Week 48 (n = 26). Genotypic resistance testing by ultra-deep sequencing (UDS) for reverse transcriptase (RT) and integrase regions was performed at baseline and at the time of VR. RESULTS In this study, 19 patients experienced VR, with 2 patients having virological failure (VF; two consecutive VLs >50 copies/mL). For the first patient with VF, UDS detected minority resistant variants only in RT (K103N, 9.6%; Y181C, 4.9%) at baseline. Some RT variants became dominant at VF (K101E, 86.3%; Y181C, 100.0%; G190A, 100.0%) and others emerged in integrase (Y143C, 2.4%; Q148R, 6.2%; N155H, 18.8%). For the second patient with VF, neither RT nor integrase mutations were detected at baseline and VF. Median HIV-DNA level was similar at baseline, Week 48 and Week 96 (2.17, 2.06 and 2.11 log10 copies/106 cells, respectively). Only one patient had a detectable seminal HIV VL (505 copies/mL). CONCLUSIONS The dual etravirine/raltegravir regimen as maintenance therapy was effective and the emergence of mutations in cases of VF was similar to that seen in other dual-regimen studies. No HIV-DNA level modification was evidenced by Week 96.
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Affiliation(s)
- Cathia Soulie
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
| | - Lambert Assoumou
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75013 Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
| | - Sophie Sayon
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
| | - Thuy Nguyen
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
| | - Marc-Antoine Valantin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Service de maladies infectieuses, F75013 Paris, France
| | - Lydie Beniguel
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75013 Paris, France
| | | | - Chakib Alloui
- AP-HP, Hôpital Avicennes, Service de Virologie, Bobigny, France
| | | | - Véronique Avettand-Fenoel
- AP-HP, Hôpital Necker, Service de Virologie, Institut Cochin - CNRS 8104/INSERM U1016/Université Paris Descartes, Paris, France
| | | | - Diane Descamps
- Sorbonne Paris Cité, INSERM, IAME, UMR 1137, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | | | - Jacques Reynes
- CHU Montpellier, Département de maladies infectieuses, Montpellier, France
| | - Gilles Peytavin
- AP-HP, Laboratoire de Pharmacologie-Toxicologie, Hôpital Bichat-Claude Bernard and IAME, UMR 1137, Sorbonne Paris Cité and INSERM, Université Paris Diderot, Paris, France
| | - Dominique Costagliola
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F75013 Paris, France
| | - Christine Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Service de maladies infectieuses, F75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié Salpêtrière - Charles Foix, laboratoire de virologie, F75013 Paris, France
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13
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Yusuf AA, Musa BM, Galadanci NA, Babashani M, Mohammed AZ, Ingles DJ, Fogo AB, Wester CW, Aliyu MH. HIV-associated nephropathy: Protocol and rationale for an exploratory genotype-phenotype study in a sub-Saharan African population. PLoS One 2021; 16:e0249567. [PMID: 33822824 PMCID: PMC8023480 DOI: 10.1371/journal.pone.0249567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 03/05/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND HIV-positive persons of African descent are disproportionately affected by chronic kidney disease (CKD). Deterioration to end-stage kidney disease (ESKD) also occurs in this population at a higher frequency. There remains a lot to learn about the genetic susceptibility to CKD in HIV positive patients, and the pathophysiology of progression to ESKD. OBJECTIVES We will conduct an exploratory genotype-phenotype study in HIV-positive persons with CKD in Aminu Kano Teaching Hospital, Nigeria, to determine blood-based differential gene expression biomarkers in different kidney risk groups according to the KDIGO 2012 criteria. METHODS We will consecutively screen 150 HIV-positive adults (≥18 years of age) attending the HIV clinic of Aminu Kano Teaching Hospital, Kano, Nigeria, for CKD based on proteinuria and elevation of estimated glomerular filtration rate. Among these, two separate groups of 16 eligible participants each (n = 32) will be selected in the four (4) KDIGO 2012 kidney risk categories. The groups will be matched for age, sex, viral suppression level and antiretroviral (ARV) regimen. In the first group (n = 16), we will determine differential gene expression markers in peripheral blood mononuclear cells using mRNA-sequencing (RNA-Seq). We will validate the differential expression markers in the second group (n = 16) using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Using a systems-based approach, we will construct, visualize and analyze gene-gene interaction networks to determine the potential biological roles of identified differential expression markers based on published literature and publicly available databases. RESULTS Our exploratory study will provide valuable information on the potential roles of differential expression biomarkers in the pathophysiology of HIV-associated kidney disease by identifying novel biomarkers in different risk categories of CKD in a sub-Saharan African population. The results of this study will provide the basis for population-based genome-wide association studies to guide future personalized medicine approaches. CONCLUSION Validated biomarkers can be potential targets for the development of stage-specific therapeutic interventions, an essential paradigm in precision medicine.
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Affiliation(s)
- Aminu Abba Yusuf
- Department of Haematology and Blood Transfusion, Bayero University Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Baba Maiyaki Musa
- Department of Medicine, Bayero University Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
- Africa Center of Excellence for Population Health and Policy
| | - Najibah Aliyu Galadanci
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, United States of America
| | - Musa Babashani
- Department of Medicine, Bayero University Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Aminu Zakari Mohammed
- Department of Histopathology, Bayero University Kano/Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Donna J. Ingles
- Vanderbilt Institute of Global Health (VIGH), Nashville, Tennessee, United States of America
| | - Agnes B. Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - C. William Wester
- Vanderbilt Institute of Global Health (VIGH), Nashville, Tennessee, United States of America
| | - Muktar Hassan Aliyu
- Vanderbilt Institute of Global Health (VIGH), Nashville, Tennessee, United States of America
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14
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Villalobos C, Ceballos ME, Ferrés M, Palma C. Drug resistance mutations in proviral DNA of HIV-infected patients with low level of viremia. J Clin Virol 2020; 132:104657. [PMID: 33049643 DOI: 10.1016/j.jcv.2020.104657] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/27/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Camila Villalobos
- Infectious Diseases Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile; Infectious Diseases Service, Hospital Naval Almirante Nef, Chile.
| | - María Elena Ceballos
- Infectious Diseases Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile.
| | - Marcela Ferrés
- Pediatric Infectious Diseases and Inmunology Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile; Infectology and Molecular Virology Laboratory, Red Salud UC CHRISTUS, Chile.
| | - Carlos Palma
- Infectology and Molecular Virology Laboratory, Red Salud UC CHRISTUS, Chile.
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15
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Simplification to High Genetic Barrier 2-Drug Regimens in People Living With HIV Harboring 4-Class Resistance Enrolled in the PRESTIGIO Registry. J Acquir Immune Defic Syndr 2020; 84:e24-e28. [PMID: 32598119 DOI: 10.1097/qai.0000000000002378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Meybeck A, Alidjinou EK, Huleux T, Boucher A, Tetart M, Choisy P, Bocket L, Ajana F, Robineau O. Virological Outcome After Choice of Antiretroviral Regimen Guided by Proviral HIV-1 DNA Genotyping in a Real-Life Cohort of HIV-Infected Patients. AIDS Patient Care STDS 2020; 34:51-58. [PMID: 32049556 DOI: 10.1089/apc.2019.0198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Issues have been raised concerning clinical relevance of HIV-1 proviral DNA genotypic resistance test (DNA GRT). To assess impact of DNA GRT on choice of antiretroviral therapy (ART) and subsequent virological outcome, we retrospectively reviewed decision-making and viral load (VL) evolution following DNA GRT performed in our center between January 2012 and December 2017, except those prescribed within the framework of a clinical trial. A total of 304 DNA GRTs were included, 185 (62%) performed in a context of virological success. Only 34% of tests were followed by ART change, more frequently in situation of virological success (39% vs. 26%, p = 0.02). In this situation, ART change guided by DNA GRT led to VL >20 copies/mL after 6 months in 5% of cases. In multivariate analysis, higher HIV DNA quantification (p = 0.01) was associated with occurrence of viremia. A higher nadir of CD4 count (p = 0.04) and a longer time with VL <20 copies/mL (p = 0.04) were independently associated with a lower risk of viremia. In situation of low-level viremia, ART change guided by DNA GRT led to VL <20 copies/mL after 6 months in 52% of cases, while decision to maintain the same treatment led to VL <20 copies/mL in 74% of cases. In multivariate analysis, longer time with VL >20 copies/mL (p = 0.02) was associated with persistence of virological replication. In conclusion, in situation of virological success, use of DNA GRT in addition to analysis of historical RNA GRT to guide ART optimization appears safe. Its prescription framework in situation of low-level viremia deserves to be better defined.
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Affiliation(s)
- Agnès Meybeck
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | | | - Thomas Huleux
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Anne Boucher
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Macha Tetart
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Philippe Choisy
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Laurence Bocket
- Virology Department, Lille University Hospital, Lille, France
| | - Faiza Ajana
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
| | - Olivier Robineau
- Infectious Diseases Department, Tourcoing Hospital, Tourcoing, France
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17
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Raymond S, Nicot F, Abravanel F, Minier L, Carcenac R, Lefebvre C, Harter A, Martin-Blondel G, Delobel P, Izopet J. Performance evaluation of the Vela Dx Sentosa next-generation sequencing system for HIV-1 DNA genotypic resistance. J Clin Virol 2019; 122:104229. [PMID: 31809945 DOI: 10.1016/j.jcv.2019.104229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 11/20/2022]
Abstract
BACKGROUND Patients on antiretroviral therapy could benefit from HIV-1 DNA resistance genotyping for exploring virological failure with low viral load or to guide treatment simplification. Few new generation sequencing data are available. OBJECTIVE To check that the automated deep sequencing Sentosa platform (Vela DX) detected minority resistant variants well enough for HIV DNA genotyping. STUDY DESIGN We evaluated the Sentosa SQ HIV genotyping assay with automated extraction on 40 DNA longitudinal samples from treatment-experienced patients by comparison with Sanger sequencing. HIV drug resistance was interpreted using the ANRS algorithm (v29) at the threshold of 20 % and 3 %. RESULTS The Sentosa SQ HIV genotyping assay was 100 % successful to amplify and sequence PR and RT and 86 % to amplify and sequence IN when the HIV DNA load was >2.5 log copies/million cells. The Sentosa and Sanger sequencing were concordant for predicting PR-RT resistance at the threshold of 20 % in 14/18 samples successfully sequenced. A higher level of resistance was predicted by Sentosa in three samples and by Sanger in one sample. The prevalence of resistance was 7 % to PI, 59 % to NRTI, 31 % to NNRTI and 20 % to integrase inhibitors using the Sentosa SQ genotyping assay at the threshold of 3 %. Seven additional mutations <20 % were detected using the Sentosa assay. CONCLUSION Automated DNA extraction and sequencing using the Sentosa SQ HIV genotyping assay accurately predicted HIV DNA drug resistance by comparison with Sanger. Prospective studies are needed to evaluate the clinical interest of HIV DNA genotyping.
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Affiliation(s)
- Stéphanie Raymond
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France.
| | - Florence Nicot
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Florence Abravanel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Luce Minier
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Romain Carcenac
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Caroline Lefebvre
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Agnès Harter
- CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
| | - Guillaume Martin-Blondel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Pierre Delobel
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Service des Maladies Infectieuses et Tropicales, Toulouse, F-31300 France
| | - Jacques Izopet
- INSERM U1043, CNRS UMR 5282, Toulouse University Paul Sabatier, CPTP, Toulouse, F-31300 France; CHU de Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, F-31300 France
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18
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Fernandez C, van Halsema CL. Evaluating cabotegravir/rilpivirine long-acting, injectable in the treatment of HIV infection: emerging data and therapeutic potential. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2019; 11:179-192. [PMID: 31447590 PMCID: PMC6682757 DOI: 10.2147/hiv.s184642] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022]
Abstract
Cabotegravir and rilpivirine long-acting injectable antiretroviral therapy for the treatment of HIV-1 infection brings promise of a new mode of delivery and potential solutions to some problems of oral therapy, but also new challenges and unanswered questions. Adding to the increasing body of evidence for newer two-drug combinations, phase II and phase III trial data to date demonstrate cabotegravir and rilpivirine combination injectable therapy to be non-inferior to selected oral triple-therapy alternatives. Most importantly, this therapy is reported to be acceptable to individuals taking the 4-weekly or 8-weekly injections, despite frequent injection-site reactions. Key outstanding questions include management of missed or delayed dosing, drug interactions and management of virological failure, as well as the efficacy of cabotegravir and rilpivirine in all HIV-1 subtypes. We describe clinical evidence to date and efficacy and challenges in selected populations, including women; those with prior virological failure; individuals with a history of difficulty adhering to oral therapy and individuals with co-infections. We await real-world data and longer-term evidence while moving forward to this new era of antiretroviral therapy.
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Affiliation(s)
- Cristina Fernandez
- Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester, UK
| | - Clare L van Halsema
- Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester, UK.,Faculty of Education, Liverpool School of Tropical Medicine, Liverpool, UK
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