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Mazouz F, Bertine M, Coppée R, Storto A, Katlama C, Landman R, Cabié A, Peytavin G, Raffi F, Yazdanpanah Y, Descamps D, Joly V, Ghosn J, Charpentier C. Proportion of APOBEC3-induced defective HIV DNA after 1 year of dolutegravir + lamivudine simplification in the ANRS 167 LAMIDOL trial. J Antimicrob Chemother 2023; 78:2995-3002. [PMID: 37930812 DOI: 10.1093/jac/dkad344] [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: 06/06/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Hypermutated viruses induced by APOBEC3 (apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3) proteins comprise some of the defective viruses in the HIV reservoir. Here, we assessed the proportion of APOBEC3-induced defective proviruses in HIV-positive patients before and after receiving dolutegravir + lamivudine dual therapy. METHODS PBMCs of virologically suppressed patients enrolled in the ANRS 167 LAMIDOL trial, evaluating a switch from triple therapy to dolutegravir + lamivudine, were collected 8 weeks before (W-8) and 48 weeks after (W48) dual-therapy initiation. The Vif and RT regions were subject to next-generation sequencing. Bioinformatic algorithms were developed to identify APOBEC3-defective sequences and APOBEC3-related drug resistance mutations (APOMuts). All hypermutated sequences and those containing at least one stop codon were considered as defective. RESULTS One hundred and four patients were enrolled (median virological suppression duration: 4.2 years; IQR: 2.0-9.1). Proviral defective reads at W-8 and W48 were detected in Vif in 22% and 29% of patients, respectively, and in RT in 38% and 42% of patients, respectively. At least one APOMut was present in proviruses of 27% and 38% of patients at W-8 and W48, respectively. The ratio of APOMuts/number of potential APOMut sites was significantly higher at W48 (16.5%) than at W-8 (9.8%, P = 0.007). The presence of APOBEC3-defective viruses at W-8 was not associated with HIV total DNA level, nor with the third drug class received prior to switching to dolutegravir + lamivudine, nor with the duration of virological suppression. CONCLUSIONS Whereas no significant change in the proportion of patients with APOBEC3-defective proviruses was evidenced after 1 year of dolutegravir + lamivudine maintenance, enrichment in APOMuts was observed. Further longer-term studies are needed to assess the other forms of defective viruses with dual-therapy.
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Affiliation(s)
- Fella Mazouz
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Mélanie Bertine
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Romain Coppée
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Alexandre Storto
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Christine Katlama
- Service de Maladies Infectieuses et Tropicales, Hôpital Pitié-Salpêtrière, Sorbonne Université, Paris, France
| | - Roland Landman
- Service de Maladies Infectieuses et Tropicales, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - André Cabié
- Service de Maladies Infectieuses et Tropicales, CHU Martinique, Fort-de-France, France
| | - Gilles Peytavin
- Service de Pharmacologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - François Raffi
- Service de Maladies Infectieuses et Tropicales, CHU Hôtel-Dieu, Nantes, France
| | - Yazdan Yazdanpanah
- Service de Maladies Infectieuses et Tropicales, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Diane Descamps
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Véronique Joly
- Service de Maladies Infectieuses et Tropicales, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Jade Ghosn
- Service de Maladies Infectieuses et Tropicales, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
| | - Charlotte Charpentier
- Service de Virologie, INSERM, IAME, UMR 1137, AP-HP, Hôpital Bichat-Claude Bernard, Université Paris Cité, Paris, France
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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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Saladini F, Giammarino F, Maggiolo F, Ferrara M, Cenderello G, Celesia BM, Martellotta F, Spagnuolo V, Corbelli GM, Gianotti N, Santoro MM, Rusconi S, Zazzi M, Castagna A. Residual phenotypic susceptibility to doravirine in multidrug-resistant HIV-1 from subjects enrolled in the PRESTIGIO Registry. Int J Antimicrob Agents 2023; 61:106737. [PMID: 36708743 DOI: 10.1016/j.ijantimicag.2023.106737] [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: 10/24/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023]
Abstract
OBJECTIVES Doravirine shows a rather distinct resistance profile within the nonnucleoside reverse transcriptase inhibitor (NNRTI) class. This study aimed to evaluate the phenotypic susceptibility to doravirine, rilpivirine and etravirine in a panel of multidrug-resistant (MDR) HIV-1 isolates collected from people living with HIV (PLWH) enrolled in the PRESTIGIO Registry. METHODS Recombinant viruses expressing PLWH-derived protease, reverse transcriptase coding regions were generated from plasma samples at virological failure with documented resistance to protease inhibitors, nucleoside reverse transcriptase inhibitors, NNRTIs and integrase strand transfer inhibitors. In vitro susceptibility was assessed through a phenotypic assay measuring fold-change values with respect to the reference NL4-3 virus. Genotypic susceptibility was computed by the Stanford HIVdb algorithm 8.9-1. RESULTS Plasma samples were collected from 22 PLWH: 20 (91%) were male, median age 55 years (IQR 50-58), time since HIV-1 diagnosis 27 years (23-31) and time on antiretroviral treatment 23 years (22-26). Median doravirine, etravirine and rilpivirine fold-change values were 9.8 (2.9-40.4), 42.9 (3.1-100.0) and 100.0 (17.9-100.0), respectively. According to the fold-change cut-offs, full susceptibility was observed in five (23%), four (18%) and one (5%) cases with doravirine, etravirine and rilpivirine, respectively. Irrespective of the presence of specific doravirine mutations, higher numbers of NNRTI mutations correlated with higher fold-change values for doravirine. By comparing the distribution of fold-change values with the Stanford HIVdb predicted susceptibility, a significant correlation was detected for doravirine and rilpivirine but not etravirine. CONCLUSION Despite extensive cross-resistance among NNRTIs, doravirine can be a valid option in a proportion of PLWH with MDR HIV-1. Doravirine activity appeared to be inferred with fair accuracy by the HIVdb algorithm.
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Affiliation(s)
- Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
| | | | | | - Micol Ferrara
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | | | | | | | | | | | | | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Antonella Castagna
- San Raffaele Scientific Institute, Milan, Italy; San Raffaele Vita-Salute University, Milan, Italy
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Mohamed S, Boulmé R, Sayada C. From Capillary Electrophoresis to Deep Sequencing: An Improved HIV-1 Drug Resistance Assessment Solution Using In Vitro Diagnostic (IVD) Assays and Software. Viruses 2023; 15:v15020571. [PMID: 36851783 PMCID: PMC9965321 DOI: 10.3390/v15020571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Drug-resistance mutations were mostly detected using capillary electrophoresis sequencing, which does not detect minor variants with a frequency below 20%. Next-Generation Sequencing (NGS) can now detect additional mutations which can be useful for HIV-1 drug resistance interpretation. The objective of this study was to evaluate the performances of CE-IVD assays for HIV-1 drug-resistance assessment both for target-specific and whole-genome sequencing, using standardized end-to-end solution platforms. METHODS A total of 301 clinical samples were prepared, extracted, and amplified for the three HIV-1 genomic targets, Protease (PR), Reverse Transcriptase (RT), and Integrase (INT), using the CE-IVD DeepChek® Assays; and then 19 clinical samples, using the CE-IVD DeepChek® HIV Whole Genome Assay, were sequenced on the NGS iSeq100 and MiSeq (Illumina, San Diego, CA, USA). Sequences were compared to those obtained by capillary electrophoresis. Quality control for Molecular Diagnostics (QCMD) samples was added to validate the clinical accuracy of these in vitro diagnostics (IVDs). Nineteen clinical samples were then tested with the same sample collection, handling, and measurement procedure for evaluating the use of NGS for whole-genome HIV-1. Sequencing analyzer outputs were submitted to a downstream CE-IVD standalone software tailored for HIV-1 analysis and interpretation. RESULTS The limits of range detection were 1000 to 106 cp/mL for the HIV-1 target-specific sequencing. The median coverage per sample for the three amplicons (PR/RT and INT) was 13,237 reads. High analytical reproducibility and repeatability were evidenced by a positive percent agreement of 100%. Duplicated samples in two distinct NGS runs were 100% homologous. NGS detected all the mutations found by capillary electrophoresis and identified additional resistance variants. A perfect accuracy score with the QCMD panel detection of drug-resistance mutations was obtained. CONCLUSIONS This study is the first evaluation of the DeepChek® Assays for targets specific (PR/RT and INT) and whole genome. A cutoff of 3% allowed for a better characterization of the viral population by identifying additional resistance mutations and improving the HIV-1 drug-resistance interpretation. The use of whole-genome sequencing is an additional and complementary tool to detect mutations in newly infected untreated patients and heavily experienced patients, both with higher HIV-1 viral-load profiles, to offer new insight and treatment strategies, especially using the new HIV-1 capsid/maturation inhibitors and to assess the potential clinical impact of mutations in the HIV-1 genome outside of the usual HIV-1 targets (RT/PR and INT).
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Affiliation(s)
| | | | - Chalom Sayada
- Advanced Biological Laboratories (ABL), 2550 Luxembourg, Luxembourg
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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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