1
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Andre-Garnier E, Bocket L, Bourlet T, Hocqueloux L, Lepiller Q, Maillard A, Reigadas S, Barriere G, Durand F, Montes B, Stefic K, Marcelin AG. Use of genotypic HIV DNA testing: a DELPHI-type consensus. J Antimicrob Chemother 2024; 79:578-588. [PMID: 38269616 PMCID: PMC10904721 DOI: 10.1093/jac/dkae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES As many disparities in the clinical use of HIV DNA sequencing are observed, a DELPHI-type consensus was initiated in France to homogenize use, techniques and interpretation of results. METHODS Based on a literature review and clinical experience, a steering committee (SC) of eight virologists and one infectious disease specialist formulated statements. Statements were submitted to an independent and anonymous electronic vote of virologists and HIV clinicians in France, between October 2022 and December 2022. RESULTS The SC developed 20 statements grouped into six categories: clinical situations for the use of HIV DNA genotyping; techniques for performing HIV DNA genotyping; consideration of apolipoprotein B mRNA editing enzyme (APOBEC) mutations; genotyping results reporting; recycling of antiretrovirals; and availability of HIV DNA genotyping tests and delays. Twenty-one virologists and 47 clinicians participated in two voting rounds and 18/20 (90%) assertions reached a 'strong' consensus. For example, that prior genotyping on HIV DNA is useful for clinical decision-making when considering switching to some long-acting regimens or to reduce the number of antiretroviral agents in virologically suppressed patients for whom RNA data are unavailable/not exploitable/not sufficiently informative. Two statements achieved no consensus: reporting any detected viral minority population for discussion in multidisciplinary meetings (virologists), and possible risk of virological failure when using a second-generation InSTI plus lamivudine or emtricitabine regimen in patients with undetectable viral load within ≥1 year and in the presence of a documented M184V mutation within the last 5 years (clinicians). CONCLUSIONS This DELPHI-type consensus will facilitate the strengthening and harmonization of good practice when performing HIV DNA sequencing.
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Affiliation(s)
| | - Laurence Bocket
- Virology Department, University Hospital Lille, Lille, France
| | - Thomas Bourlet
- Infectious Agents and Hygiene Department, University Hospital of Saint Etienne, Saint-Etienne, France
| | - Laurent Hocqueloux
- Infectious and Tropical Diseases Department, University Hospital Orléans, Orléans, France
| | - Quentin Lepiller
- Virology Department, University Hospital Besançon, Besançon, France
| | - Anne Maillard
- Virology Department, University Hospital Rennes, Rennes, France
| | | | | | | | - Brigitte Montes
- Virology Department, University Hospital Montpellier, Montpellier, France
| | - Karl Stefic
- Bacteriology, Virology and Hospital Hygene Department, University of Tours, INSERM U1259 MAVIVH, University Hospital Tours, Tours, France
| | - Anne-Geneviève Marcelin
- Virology Departement, Sorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, AP-HP, University Hospitals Pitié-Salpêtrière—Charles Foix, 83, Boulevard de l’hôpital, Paris 75013, France
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2
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Lan Y, Ling X, Deng X, Lin Y, Li J, Li L, He R, Cai W, Li F, Li L, Hu F. Drug Resistance Profile Among HIV-1 Infections Experiencing ART with Low-Level Viral Load in Guangdong China During 2011-2022: A Retrospective Study. Infect Drug Resist 2023; 16:4953-4964. [PMID: 37546367 PMCID: PMC10402888 DOI: 10.2147/idr.s419610] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/27/2023] [Indexed: 08/08/2023] Open
Abstract
Background Antiretroviral therapy (ART) efficiently reduces the morbidities and mortalities caused by HIV-1 infection and prevents the HIV epidemic. However, virologic failure (VF) occurs in some patients receiving ART experience, especially increases in those patients with intermittent or persistent low-level viremia (LLV). The presence of drug resistance mutations (DRMs) in LLV was a strong predictor of subsequent VF. The data on drug resistance (DR) or DRMs for HIV-1 infections at low-level viral load (LLVL) are limited in China. Objective To monitor the prevalence of HIV-1 drug resistance and to evaluate the risk factors associated with drug resistance in LLVL HIV-1 infections during ART in Guangdong, China. Methods Plasma samples with LLVL during ART in Guangdong Province between Jan 2011 and Dec 2022 were subjected to a modified reverse-transcription PCR with a pre-step of virus concentration by ultracentrifugation before extraction and the Sanger sequencing. Then, the genotypic resistance test was performed and DR was analyzed by the Stanford HIVDB program. Finally, DR-associated factors were identified by logistic regression analysis. Results We found that CRF01_AE (53.57%) and CRF07_BC (25.07%) were the dominant HIV-1 genotypes in LLVL in Guangdong between 2011 and 2022 but that the percentage of CRF01_AE showed a trend of decrease over time. M46 (1.49%), M184 (30.91%), and K103 (21.46%) were the dominant PI-, NRTI-, and NNRTI-associated mutations, respectively. The total DR rate was 47.06%. Specifically, PI (3.71%) showed a significantly lower DR rate than NNRTI (40.74%) and NRTI (34.14%). Duration of ART, initial ART regimen, ethnicity, and WHO clinical stages were associated with DR. Conclusion The drug resistance rate among the LLVL during ART in Guangdong, China is high. The risk factors associated with HIV drug resistance should be seriously considered for better control.
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Affiliation(s)
- Yun Lan
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Xuemei Ling
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
- Guangdong Center for Diagnosis and Treatment of AIDS, Guangzhou, 510060, People’s Republic of China
| | - Xizi Deng
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Yaqing Lin
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Junbin Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
- Guangdong Center for Diagnosis and Treatment of AIDS, Guangzhou, 510060, People’s Republic of China
| | - Liya Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Ruiying He
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Linghua Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, 510440, People’s Republic of China
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3
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Charpentier C, Le Hingrat Q, Ferré VM, Damond F, Descamps D. Future of Antiretroviral Drugs and Evolution of HIV-1 Drug Resistance. Viruses 2023; 15:v15020540. [PMID: 36851754 PMCID: PMC9967014 DOI: 10.3390/v15020540] [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: 01/09/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Highly active antiretroviral (ARV) therapy has been used for many years, but the use in low- and middle-income countries of antiretroviral drugs with low genetic barrier to resistance, combined with limited availability of viral load testing, has led to higher rates of acquired drug resistance, sustaining the rate of transmitted drug resistance. Here, we describe the evolution of ARV drugs with the ongoing development of injectable long-acting forms and the requirements regarding all new ARV drugs (i.e., no transmitted drug resistance, no cross-resistance and high genetic barrier to resistance). Then, we report the evolution of both transmitted and acquired resistance regarding new ARV drugs. The WHO has set very ambitious but motivating goals for HIV testing, treatment and viral suppression, aiming to achieve rates of 95% for all three by 2025. Reaching these goals requires a wide implementation and use of close virological monitoring in LMICs.
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4
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Nyamankolly E, Bellecave P, Wittkop L, Le Marec F, Duffau P, Lazaro E, Vareil MO, Tumiotto C, Hessamfar M, Cazanave C, Perrier A, Leleux O, Bonnet F, Neau D. Long-term follow-up of HIV-1 multi-drug-resistant treatment-experienced participants treated with etravirine, raltegravir and boosted darunavir: towards drug-reduced regimen? ANRS CO3 Aquitaine Cohort 2007-2018. Int J Antimicrob Agents 2023; 61:106696. [PMID: 36470511 DOI: 10.1016/j.ijantimicag.2022.106696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 12/04/2022]
Abstract
OBJECTIVE To assess the efficacy of raltegravir, etravirine and darunavir/ritonavir (TRIO regimen) in treatment-experienced patients with human immunodeficiency virus-1 (HIV-1) infection by describing the proportion of patients who experienced virological failure (VF) at Week 24. The secondary objectives were to assess the HIV-1 plasma viral load (pVL) after Week 24, the proportion of patients who were receiving dual therapy or monotherapy at the last visit, and the number of deaths. METHODS Patients from the ANRS CO3 Aquitaine Cohort who were prescribed the TRIO regimen between February 2007 and September 2018 were classified into two groups based on their pVL at study inclusion: the virological failure group (VFG; pVL >50 copies/mL) and the virologically suppressed group (VSG; pVL <50 copies/mL). The impact of baseline pVL and genotypic susceptibility score (GSS) on VF was analysed. RESULTS In total, 184 patients were enrolled in this study, with 123 (66.8%) in the VFG and 61 (33.2%) in the VSG. The median length of follow-up was 7.5 (interquartile range 4.1-9.6) years, and 29 (15.8%) patients died. Thirty-seven (25.5%) patients experienced VF at Week 24, including 32/145 (32.7%) in the VFG and 5/47 (10.6%) in the VSG (P<0.01). Resistance-associated mutations were detected in integrase, reverse transcriptase and protease for 7/37 (18.9%), 3/37 (8.1%) and 1/37 (2.7%) patients, respectively. High pVL and GSS at baseline were independently associated with VF. At the last visit, 76/184 (41.3%) patients were still receiving the TRIO regimen, while 55/184 (29.9%) were receiving dual therapy and 1/184 (0.5%) was receiving protease inhibitor monotherapy. Among the 56 patients receiving dual therapy or monotherapy, 51 (96.2%) had pVL <50 copies/mL. CONCLUSION Despite a high level of mutation resistance at baseline, long-term virological follow-up was favourable and one-third of patients were eligible for drug-reducing strategies.
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Affiliation(s)
- Elsa Nyamankolly
- CHU de Bordeaux, Service des Maladies Infectieuses et Tropicales, Hôpital Pellegrin, Bordeaux, France.
| | | | - Linda Wittkop
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France; CHU de Bordeaux, Service d'information médicale, Bordeaux, France
| | - Fabien Le Marec
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France
| | - Pierre Duffau
- CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France; CHU de Bordeaux, Service de Médecine Interne, Hôpital Saint-André, Bordeaux, France
| | - Estibaliz Lazaro
- CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France; CHU de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Haut-Lévêque, Pessac, France
| | - Marc-Olivier Vareil
- CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France; CH Bayonne Service des Maladies Infectieuses, Bayonne, France
| | - Camille Tumiotto
- CHU de Bordeaux, Virology Laboratory, Bordeaux, France; Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, Bordeaux, France
| | - Mojgan Hessamfar
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France; CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France; CHU de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Saint-André, Bordeaux, France
| | - Charles Cazanave
- CHU de Bordeaux, Service des Maladies Infectieuses et Tropicales, Hôpital Pellegrin, Bordeaux, France
| | - Adélaïde Perrier
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France
| | - Olivier Leleux
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France
| | - Fabrice Bonnet
- Bordeaux Population Health Research Center, INSERM U1219, CIC-EC 1401, Univ. Bordeaux - ISPED, 33076, Bordeaux, France; CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France; CHU de Bordeaux, Service de Médecine Interne et Maladies Infectieuses, Hôpital Saint-André, Bordeaux, France
| | - Didier Neau
- CHU de Bordeaux, Service des Maladies Infectieuses et Tropicales, Hôpital Pellegrin, Bordeaux, France; CHU de Bordeaux, COREVIH Nouvelle Aquitaine, Bordeaux, France
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5
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Bareng OT, Choga WT, Maphorisa ST, Seselamarumo S, Seatla KK, Mokgethi PT, Maruapula D, Mogwele ML, Ditshwanelo D, Moraka NO, Gobe I, Motswaledi MS, Makhema JM, Musonda R, Shapiro R, Essex M, Novitsky V, Moyo S, Gaseitsiwe S. HIV-1C in-House RNA-Based Genotyping Assay for Detection of Drug Resistance Mutations in Samples with Low-Level Viral Loads. Infect Drug Resist 2022; 15:7565-7576. [PMID: 36582452 PMCID: PMC9792565 DOI: 10.2147/idr.s388816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Monitoring HIV-1 drug resistance mutations (DRM) in treated patients on combination antiretroviral therapy (cART) with a detectable HIV-1 viral load (VL) is important for the selection of appropriate cART. Currently, there is limited data on HIV DRM at low-level viremia (LLV) (VL 401-999 copies/mL) due to the use of a threshold of VL ≥1000 copies/mL for HIV DRM testing. We here assess the performance of an in-house HIV drug resistance genotyping assay using plasma for the detection of DRM at LLV. Methods We used a total of 96 HIV plasma samples from the population-based Botswana Combination Prevention Project (BCPP). The samples were stratified by VL groups: 50 samples had LLV, defined as 401-999 copies/mL, and 46 had ≥1000 copies/mL. HIV pol (PR and RT) region was amplified and sequenced using an in-house genotyping assay with BigDye sequencing chemistry. Known HIV DRMs were identified using the Stanford HIV Drug Resistance Database. Genotyping success rate between the two groups was estimated and compared using the comparison of proportions test. Results The overall genotyping success rate was 79% (76/96). For VL groups, the genotyping success was 72% (36/50) at LLV and 87% (40/46) at VL ≥1000 copies/mL. Among generated sequences, the overall prevalence of individuals with at least 1 major or intermediate-associated DRM was 24% (18/76). The proportions of NNRTI-, NRTI- and PI-associated resistance mutations were 28%, 24%, and 0%, respectively. The most predominant mutations detected were K103N (18%) and M184V (12%) in NNRTI- and NRTI-associated mutations, respectively. The prevalence of DRM was 17% (6/36) at LLV and 30% (12/40) at VL ≥1000 copies/mL. Conclusion The in-house HIV genotyping assay successfully genotyped 72% of LLV samples and was able to detect 17% of DRM amongst them. Our results highlight the possibility and clinical significance of genotyping HIV among individuals with LLV.
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Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | - Kaelo K Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Patrick T Mokgethi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Doreen Ditshwanelo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Biological Science and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | | | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Modisa S Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana,Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA,Correspondence: Simani Gaseitsiwe, Botswana Harvard AIDS Institute Partnership, Private Bag BO320, Bontleng, Gaborone, Botswana, Tel +267 390 2671, Fax +267 390 1284, Email
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6
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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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7
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Ding L, Chen X, He J, Zheng J, Wei X, Qin B, Li X. Analysis of virologic outcome in low-level HIV-1 viremia patients in a small cohort. Future Virol 2022. [DOI: 10.2217/fvl-2021-0195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: It is unclear whether a low-level viremia (LLV) status is maintained in HIV-infected patients. Materials & methods: HIV-infected patients with LLV were enrolled and followed up for 5 years. Factors associated with virological outcomes were assessed via regression analyses. Results: A total of 39 patients maintained an LLV status, whereas 19 had disease progression with a viral load of ≥1000 copies/ml. LLV duration and drug resistance (DR) were associated with virological failure. Among the DR cases, the most frequent mutations were M184V/I (70.4%) and K103N (40.7%). Protease inhibitor (PI) mutations were rare. Conclusion: There is an increased risk for virologic failure in HIV-1-infected patients maintaining LLV for a long time. DR was not a rare phenomenon in LLV patients.
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Affiliation(s)
- Lisha Ding
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Xi Chen
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Jianmei He
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Jun Zheng
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Xiuqing Wei
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Biyun Qin
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
| | - Xiangzhong Li
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha, 410005, China
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8
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Bareng OT, Moyo S, Zahralban-Steele M, Maruapula D, Ditlhako T, Mokaleng B, Mokgethi P, Choga WT, Moraka NO, Pretorius-Holme M, Mine MO, Raizes E, Molebatsi K, Motswaledi MS, Gobe I, Mohammed T, Gaolathe T, Shapiro R, Mmalane M, Makhema JM, Lockman S, Essex M, Novitsky V, Gaseitsiwe S. HIV-1 drug resistance mutations among individuals with low-level viraemia while taking combination ART in Botswana. J Antimicrob Chemother 2022; 77:1385-1395. [PMID: 35229102 PMCID: PMC9633723 DOI: 10.1093/jac/dkac056] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/03/2022] [Indexed: 10/13/2023] Open
Abstract
OBJECTIVES To assess whether a single instance of low-level viraemia (LLV) is associated with the presence of drug resistance mutations (DRMs) and predicts subsequent virological failure (VF) in adults receiving ART in 30 communities participating in the Botswana Combination Prevention Project. METHODS A total of 6078 HIV-1 C pol sequences were generated and analysed using the Stanford HIV drug resistance database. LLV was defined as plasma VL = 51-999 copies/mL and VF was defined as plasma VL ≥ 1000 copies/mL. RESULTS Among 6078 people with HIV (PWH), 4443 (73%) were on ART for at least 6 months. Of the 332 persons on ART with VL > 50 copies/mL, 175 (4%) had VL ≥ 1000 copies/mL and 157 (4%) had LLV at baseline. The prevalence of any DRM was 57 (36%) and 78 (45%) in persons with LLV and VL ≥ 1000 copies/mL, respectively. Major DRMs were found in 31 (20%) with LLV and 53 (30%) with VL ≥ 1000 copies/mL (P = 0.04). Among the 135 PWH with at least one DRM, 17% had NRTI-, 35% NNRTI-, 6% PI- and 3% INSTI-associated mutations. Among the 3596 participants who were followed up, 1709 (48%) were on ART for ≥6 months at entry and had at least one subsequent VL measurement (median 29 months), 43 (3%) of whom had LLV. The OR of experiencing VF in persons with LLV at entry was 36-fold higher than in the virally suppressed group. CONCLUSIONS A single LLV measurement while on ART strongly predicted the risk of future VF, suggesting the use of VL > 50 copies/mL as an indication for more intensive adherence support with more frequent VL monitoring.
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Affiliation(s)
- Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Melissa Zahralban-Steele
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Biological Sciences, Faculty of Science, University of Botswana, Gaborone, Botswana
| | | | - Baitshepi Mokaleng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | - Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Natasha O Moraka
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Molly Pretorius-Holme
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Madisa O Mine
- Botswana Ministry of Health and Wellness, Gaborone, Botswana
| | - Elliot Raizes
- U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Statistics, University of Botswana, Gaborone, Botswana
| | - Modisa S Motswaledi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Irene Gobe
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | | | | | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mompati Mmalane
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Joseph M Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Brigham and Women’s Hospital, Boston, MA, USA
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Vlad Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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9
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Abstract
HIV-1 is genetically heterogeneous, having different subtypes and circulating recombinant forms (CRFs). HIV-1 genotyping is used to determine drug resistance profiles and is based on the use of a mixture of consensus and degenerate primers targeting the pol gene. However, the use of this type of primers is associated with either PCR bias or PCR failure. Consensus-degenerate hybrid oligonucleotide primers (CODEHOPs) can detect and identify unknown and distantly related gene sequences by PCR. CODEHOPs designed using different HIV-1 subtypes and CRFs were evaluated for HIV-1 genotyping by Sanger and MinION sequencing. A total of 321 plasma samples were used for the validation of CODEHOP-mediated HIV-1 genotyping. CODEHOP-mediated PCR showed 100% sensitivity and specificity, with limits of detection and genotyping below 200 copies/ml. The head-to-head evaluation of CODEHOP-mediated PCR and standard PCR showed 97 to 98% and 82 to 84% PCR success rates, respectively. There was 100% agreement between the CODEHOP and the reference method in the drug resistance profiles determined by Sanger-based sequencing. Using MinION sequencing, the CODEHOP-mediated PCR scheme resulted in better depth of genome coverage and detection of more drug resistance variants in the protease and reverse transcriptase genes than the standard amplification scheme. The overall prevalences of drug resistance mutations were 17.1% in treatment-experienced patients and 1.2% in treatment-naive patients. They were mainly associated with resistance to reverse transcriptase inhibitors and were linked to virological failure and the patient’s treatment history. Findings from this study suggest that the performance of HIV-1 genotyping is improved by using CODEHOP-mediated PCR. IMPORTANCE HIV-1 drug resistance is the main cause of treatment failure. Regular surveillance of resistance-associated mutations in HIV-1 genomes is essential for the optimal management of HIV-1 infections. Due to HIV-1’s genetic diversity, different HIV-1 genotypes are circulating worldwide. Standard primers used in the amplification of HIV-1 RNA have not been designed to cover all HIV-1 genotypes and are the main cause of amplification and drug resistance test failure. In this study, new sets of PCR primers targeting the protease, reverse transcriptase, and integrase genes were designed using the CODEHOP approach. They were compared to primers recommended in part by WHO for drug resistance testing using in-house PCR. Unsuccessful HIV-1 RNA amplification was less likely to occur with CODEHOP primers, leading to fewer test failures and lower cost. Furthermore, CODEHOP primers were more effective than standard primers for the detection of minority resistant variants by MinION sequencing.
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10
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Abdi B, Chebbi M, Wirden M, Teyssou E, Sayon S, Palich R, Seang S, Valantin MA, Simon A, Tubiana R, Katlama C, Calvez V, Marcelin AG, Soulie C. No difference in HIV-1 integrase inhibitor resistance between CSF and blood compartments. J Antimicrob Chemother 2021; 76:1553-1557. [PMID: 33693680 DOI: 10.1093/jac/dkab064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/10/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Little is known about HIV-1 integrase inhibitor resistance in the CNS. OBJECTIVES This study aimed to evaluate integrase inhibitor resistance in CSF, as a marker of the CNS, and compare it with the resistance in plasma. METHODS HIV integrase was sequenced both in plasma and CSF for 59 HIV-1 patients. The clinical and biological data were collected from clinical routine care. RESULTS Among the 59 HIV-1 patients, 32 (54.2%) were under antiretroviral (ARV) treatment. The median (IQR) HIV-1 RNA in the plasma of viraemic patients was 5.32 (3.85-5.80) and 3.59 (2.16-4.50) log10 copies/mL versus 4.79 (3.56-5.25) and 3.80 (2.68-4.33) log10 copies/mL in the CSF of ARV-naive and ARV-treated patients, respectively. The patients were mainly infected with non-B subtypes (72.2%) with the most prevalent recombinant form being CRF02_AG (42.4%). The HIV-1 integrase sequences from CSF presented resistance mutations for 9/27 (33.3%) and 8/32 (25.0%) for ARV-naive (L74I, n = 3; L74I/M, n = 1; T97A, n = 1; E157Q, n = 4) and ARV-treated (L74I, n = 6; L74M, n = 1; T97A, n = 1; N155H, n = 1) patients, respectively. Integrase inhibitor resistance mutations in CSF were similar to those in plasma, except for 1/59 patients. CONCLUSIONS This work shows similar integrase inhibitor resistance profiles in the CNS and plasma in a population of HIV-1 viraemic patients.
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Affiliation(s)
- 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
| | - Mouna Chebbi
- 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 Wirden
- 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
| | - Elisa Teyssou
- 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
| | - Romain Palich
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Service de Maladies Infectieuses, F75013, Paris, France
| | - Sophie Seang
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Service de Maladies Infectieuses, F75013, Paris, France
| | - Marc-Antoine Valantin
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Service de Maladies Infectieuses, F75013, Paris, France
| | - Anne Simon
- AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Service de Médecine Interne, F75013 Paris, France
| | - Roland Tubiana
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, Service de Maladies Infectieuses, F75013, Paris, France
| | - Christine Katlama
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix, 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
| | - 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
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11
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Armenia D, Di Carlo D, Flandre P, Bouba Y, Borghi V, Forbici F, Bertoli A, Gori C, Fabeni L, Gennari W, Pinnetti C, Mondi A, Cicalini S, Gagliardini R, Vergori A, Bellagamba R, Malagnino V, Montella F, Colafigli M, Latini A, Marocco R, Licthner M, Andreoni M, Mussini C, Ceccherini-Silberstein F, Antinori A, Perno CF, Santoro MM. HIV MDR is still a relevant issue despite its dramatic drop over the years. J Antimicrob Chemother 2021; 75:1301-1310. [PMID: 31976521 DOI: 10.1093/jac/dkz554] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/16/2019] [Accepted: 12/11/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES To evaluate the prevalence and therapeutic relevance of drug resistance among isolates from ART-experienced HIV-1-infected patients over the past two decades in Italy. METHODS Dynamics of resistance to one, two and three or more antiretroviral classes were evaluated from 1999-2018. Virological success (VS) after the latest therapy switch was evaluated according to cumulative class resistance and cumulative genotypic susceptibility score (Stanford HIV_DB algorithm). RESULTS Among 13 663 isolates (from 6739 patients), resistance to at least one drug class decreased sharply from 1999 to 2010 (≤2001, 84.6%; 2010, 43.6%; P < 0.001), then remained relatively constant at ∼40% during 2010-18, with the proportion of resistance to three or more classes also stable (∼5%). After 2008, integrase inhibitor resistance slightly increased from 5.6% to 9.7% in 2018 and contributed to resistance, particularly in isolates with resistance to three or more classes (one class, 8.4%; two classes, 15.3%; three or more classes, 34.7%, P < 0.001). Among 1827 failing patients with an available follow-up, by 1 year after genotype-guided therapy start the probability of VS was 87.6%. Patients with cumulative resistance to three or more classes and receiving a poorly active regimen showed the lowest probability (62.6%) of VS (P < 0.001) compared with all other patients (≥81.8%). By Cox regression analysis, cumulative MDR and receiving poorly active antiretroviral regimens were associated with a lower hazard of VS compared with those without resistance. CONCLUSIONS A dramatic drop of HIV-1 drug resistance at failure has been achieved over the last two decades in Italy; resistance to three or more classes is low but present among currently failing patients. Its management still requires a rational and careful diagnostic and therapeutic approach.
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Affiliation(s)
- D Armenia
- UniCamillus International University of Health and Medical Sciences, Rome, Italy.,University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy
| | - D Di Carlo
- University of Milan, Pediatric Clinical Research Center 'Romeo and Enrica Invernizzi', Milan, Italy
| | - P Flandre
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP) équipe Epidémiologie clinique des maladies virales chroniques, Paris, France
| | - Y Bouba
- University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy.,Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon
| | - V Borghi
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - F Forbici
- Laboratory of Virology, National Institute for Infectious Diseases 'Lazzaro Spallanzani', IRCCS, Rome, Italy
| | - A Bertoli
- University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy
| | - C Gori
- Laboratory of Virology, National Institute for Infectious Diseases 'Lazzaro Spallanzani', IRCCS, Rome, Italy
| | - L Fabeni
- University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy
| | - W Gennari
- Microbiology Unit, University Hospital of Modena, Modena, Italy
| | - C Pinnetti
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - A Mondi
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - S Cicalini
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - R Gagliardini
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - A Vergori
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - R Bellagamba
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - V Malagnino
- Clinical Infectious Diseases, University Hospital 'Tor Vergata', Rome, Italy
| | - F Montella
- Infectious disease Unit, San Giovanni Addolorata Hospital, Rome, Italy
| | - M Colafigli
- Unit of Dermatology and Sexually Transmitted Diseases, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - A Latini
- Unit of Dermatology and Sexually Transmitted Diseases, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - R Marocco
- Infectious Diseases Unit, 'Sapienza' University, Polo Pontino, Latina, Italy
| | - M Licthner
- Infectious Diseases Unit, 'Sapienza' University, Polo Pontino, Latina, Italy
| | - M Andreoni
- Clinical Infectious Diseases, University Hospital 'Tor Vergata', Rome, Italy
| | - C Mussini
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | | | - A Antinori
- HIV/AIDS Department, National Institute for Infectious Diseases 'Lazzaro Spallanzani' IRCCS, Rome, Italy
| | - C F Perno
- Laboratory of Virology, National Institute for Infectious Diseases 'Lazzaro Spallanzani', IRCCS, Rome, Italy
| | - M M Santoro
- University of Rome 'Tor Vergata', Department of Experimental Medicine, Rome, Italy
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12
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Blanch-Lombarte O, Santos JR, Peña R, Jiménez-Moyano E, Clotet B, Paredes R, Prado JG. HIV-1 Gag mutations alone are sufficient to reduce darunavir susceptibility during virological failure to boosted PI therapy. J Antimicrob Chemother 2021; 75:2535-2546. [PMID: 32556165 PMCID: PMC7443716 DOI: 10.1093/jac/dkaa228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 05/03/2020] [Indexed: 01/01/2023] Open
Abstract
Background Virological failure (VF) to boosted PIs with a high genetic barrier is not usually linked to the development of resistance-associated mutations in the protease gene. Methods From a cohort of 520 HIV-infected subjects treated with lopinavir/ritonavir or darunavir/ritonavir monotherapy, we retrospectively identified nine patients with VF. We sequenced the HIV-1 Gag-protease region and generated clonal virus from plasma samples. We characterized phenotypically clonal variants in terms of replicative capacity and susceptibility to PIs. Also, we used VESPA to identify signature mutations and 3D molecular modelling information to detect conformational changes in the Gag region. Results All subjects analysed harboured Gag-associated polymorphisms in the absence of resistance mutations in the protease gene. Most Gag changes occurred outside Gag cleavage sites. VESPA analyses identified K95R and R286K (P < 0.01) as signature mutations in Gag present at VF. In one out of four patients with clonal analysis available, we identified clonal variants with high replicative capacity and 8- to 13-fold reduction in darunavir susceptibility. These clonal variants harboured K95R, R286K and additional mutations in Gag. Low susceptibility to darunavir was dependent on the Gag sequence context. All other clonal variants analysed preserved drug susceptibility and virus replicative capacity. Conclusions Gag mutations may reduce darunavir susceptibility in the absence of protease mutations while preserving viral fitness. This effect is Gag-sequence context dependent and may occur during boosted PI failure.
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Affiliation(s)
- Oscar Blanch-Lombarte
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - José R Santos
- Lluita contra la SIDA Foundation, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Infectious Diseases Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Ruth Peña
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Roger Paredes
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Faculty of Medicine, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Julia G Prado
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain and Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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13
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Ding L, Chen X, He J, Zheng J, Wei X. A retrospective analysis of neglected HIV-1 patients with middle-level viremia in Central China based on current policy. Future Virol 2021. [DOI: 10.2217/fvl-2020-0043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Due to the conflict of policies, HIV-1 middle-level viremia during antiretroviral therapy is neglected in China, so its clinical management was retrospectively investigated. Materials & methods: The characteristics and clinical indicators of HIV-1 patients treated in 2016 were analyzed. Results: Of 4370 cases, 1.2% progressed to middle-level viremia and 5.4% had persistent viral loads of ≥1000 copies/ml. Age, transmission mode and the ‘test and treat’ ratio among the three groups were significantly different (p < 0.05). Ordinal regression analysis showed that younger patients with higher CD4 count at baseline achieved better viral suppression if they had treatment as soon as possible. Conclusion: The results supported the ‘test and treat’ policy and suggested that the current treatment standard and testing policies should be adjusted.
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Affiliation(s)
- Lisha Ding
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha 410005, China
| | - Xi Chen
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha 410005, China
| | - Jianmei He
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha 410005, China
| | - Jun Zheng
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha 410005, China
| | - Xiuqing Wei
- Hunan Provincial Center for Diseases Control & Prevention, 450 Furongzhong Rd sec 1, Changsha 410005, China
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14
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Ndashimye E, Arts EJ. Dolutegravir response in antiretroviral therapy naïve and experienced patients with M184V/I: Impact in low-and middle-income settings. Int J Infect Dis 2021; 105:298-303. [PMID: 33722682 DOI: 10.1016/j.ijid.2021.03.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Dolutegravir (DTG) is now recommended to all HIV infected adults, adolescents, and children of right age by WHO. The low cost of $75 per year for generic DTG-based combination, has allowed 3.9 million people living with HIV (PLWH) in low and middle-income countries (LMICs) access to DTG. Lamivudine and emtricitabine associated M184V/I mutation is highly prevalent in PLWH and the majority of HIV infected individuals receiving DTG regimens may already be carrying M184V/I mutation. DISCUSSION Despite high prevalence of M184V/I in antiretroviral therapy (ART) experienced patients, DTG treatment outcomes will likely not be adversely affected by this mutation. The use of DTG in ART naïve has been largely characterised by rare emergence of resistance and virological failure. DTG-based regimens have to great extent been effective at maintaining viral suppression in treatment experienced PLWH carrying M184V/I. CONCLUSIONS Initiating patients on DTG may help preserve more treatment options for HIV infected individuals living in LMICs. High genetic barrier to the development of resistance associated with DTG and progressive viral suppression in patients switched to DTG-based therapy with M184V/I, may encourage better DTG outcomes and help in curbing increasing levels of HIV drug resistance in LMICs.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada; Joint Clinical Research Centre, Center for AIDS Research Uganda Laboratories, Kampala, Uganda.
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada.
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15
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Chaussade H, Tumiotto C, Le Marec F, Leleux O, Lefèvre L, Lazaro E, Lafon ME, Nyamankolly E, Duffau P, Neau D, Bellecave P, Bonnet F. A Low Level of Darunavir Resistance-Associated Mutation Emergence in Patients With Virological Failure During Long-term Use of Darunavir in People With HIV. The ANRS CO3 Aquitaine Cohort. Open Forum Infect Dis 2021; 7:ofaa567. [PMID: 33409332 PMCID: PMC7772944 DOI: 10.1093/ofid/ofaa567] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/18/2020] [Indexed: 11/14/2022] Open
Abstract
Background Ritonavir-boosted darunavir (DRV/r) is a protease inhibitor (PI) indicated for the treatment of naïve and pretreated HIV-infected patients since 2007. Our study aims to describe DRV/r-treated patients experiencing virological failure (VF) documented with HIV resistance testing. Methods Data from patients belonging to the ANRS CO3 Aquitaine Cohort treated with a regimen including DRV/r between February 2007 and December 2015 were analyzed. Baseline characteristics of patients experiencing VF (defined by 2 consecutive plasma viral loads >50 copies/mL) were compared with those without VF. We then described factors associated with VF as emergence of IAS DRV resistance–associated mutations (RAMs). Results Among the 1458 patients treated at least once with a DRV/r-based regimen, 270 (18.5%) patients experienced VF during follow-up, including 240 with at least 1 genotype resistance test (GRT). DRV RAMs were detected in 29 patients (12%). Among them, 25/29 patients had ≥2 DRV RAMs before DRV/r initiation, all of whom had experienced VF during previous PI treatments. For 18/29, DRV/r was maintained after VF, and controlled viremia was restored after modification of DRV-associated antiretroviral molecules or increased DRV dose. Finally, only 6/29 patients selected new DRV RAMs after DRV/r initiation. All of these experienced previous VFs while on other PIs. Conclusions These results highlight the efficacy and robustness of DRV/r, as the emergence of DRV RAMs appeared in <0.4% of patients receiving a DRV/r-based regimen in our large cohort.
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Affiliation(s)
- Hélène Chaussade
- CHU Bordeaux, Services de Médecine Interne et Maladies Infectieuses, Bordeaux, France
| | | | - Fabien Le Marec
- Univ. Bordeaux, ISPED, Inserm, Bordeaux Population Health Research Center, Team MORPH3Eus, UMR, Bordeaux, France
| | - Olivier Leleux
- Univ. Bordeaux, ISPED, Inserm, Bordeaux Population Health Research Center, Team MORPH3Eus, UMR, Bordeaux, France
| | | | - Estibaliz Lazaro
- CHU Bordeaux, Services de Médecine Interne et Maladies Infectieuses, Pessac, France
| | | | - Elsa Nyamankolly
- CHU Bordeaux, Service des Maladies Infectieuses et Tropicales, Bordeaux, France
| | - Pierre Duffau
- CHU Bordeaux, Services de Médecine Interne et Maladies Infectieuses, Bordeaux, France
| | - Didier Neau
- CHU Bordeaux, Service des Maladies Infectieuses et Tropicales, Bordeaux, France
| | | | - Fabrice Bonnet
- CHU Bordeaux, Services de Médecine Interne et Maladies Infectieuses, Bordeaux, France.,Univ. Bordeaux, ISPED, Inserm, Bordeaux Population Health Research Center, Team MORPH3Eus, UMR, Bordeaux, France
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16
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Lai A, Franzetti M, Bergna A, Saladini F, Bruzzone B, Di Giambenedetto S, Di Biagio A, Lo Caputo S, Santoro MM, Maggiolo F, Parisi SG, Rusconi S, Gianotti N, Balotta C. Marked decrease in acquired resistance to antiretrovirals in latest years in Italy. Clin Microbiol Infect 2020; 27:1038.e1-1038.e6. [PMID: 32979570 DOI: 10.1016/j.cmi.2020.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/25/2020] [Accepted: 09/15/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of this study was to evaluate acquired drug resistance in Italy in the 2009-2018 period. METHODS We analysed 3094 patients from the Italian ARCA database who had failed antiretroviral treatment and who had received a genotypic test after 6 months of treatment. Drug resistance mutations were identified using International AIDS Society (IAS)-USA tables and the Stanford HIVdb algorithm. The global burden of acquired resistance was calculated among all subjects with antiretroviral failure. Time trends and correlates of resistance were analysed using standard statistical tests. RESULTS Patients of non-European origin and non-B subtypes increased significantly from 11.5% (103/896) to 19.2% (33/172) and from 13.1% (141/1079) to 23.8% (53/223), respectively, over time. Overall, 14.5% (448/3094), 12.1% (374/3094) and 37.8% (1169/3094) of patients failed first, second and later lines, respectively. According to both IAS and HIVdb, in the study period resistance to any class, nucleoside reverse inhibitor, non-nucleoside reverse inhibitor, and protease inhibitors (PIs) declined significantly. Integrase strand transfer inhibitor (INSTI) resistance declined significantly from 31% (36/116) to 20.8% (41/197) according to HIVdb but not to IAS. Divergent data were highlighted regarding the proportion of non-European patients carrying any, PI and INSTI resistance using IAS tables compared with the Stanford HIVdb algorithm, as the former failed to detect a decrease in resistance while the latter indicates a reduction of 1.6-, 5- and 1.8-fold resistance for such drug classes. In the multivariate analysis, the risk of resistance increased in patients with a larger number of treatment lines and higher viraemia and decreased in those starting therapy in the last biennium of the study. DISCUSSION A marked reduction in drug resistance was observed over 10 years, compatible with higher genetic barrier and potency of new antiretrovirals. Nonetheless, concerns remain for subjects with non-B subtypes when using mutation lists instead of interpretation systems because of the extensive polymorphism of the protease region.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy.
| | - Marco Franzetti
- Infectious Diseases Unit, 'A. Manzoni' Hospital, Lecco, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | - Francesco Saladini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - Simona Di Giambenedetto
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart of Rome, Rome, Italy
| | - Antonio Di Biagio
- Infectious Diseases Clinic, Department of Health Sciences, University of Genoa, San Martino Hospital-IRCCS, Genoa, Italy
| | - Sergio Lo Caputo
- Clinic of Infectious Diseases, University Hospital Policlinico, University of Bari, Bari, Italy
| | | | - Franco Maggiolo
- Clinic of Infectious Diseases, Ospedali Riuniti, Bergamo, Italy
| | - Saverio G Parisi
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Stefano Rusconi
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
| | | | - Claudia Balotta
- Department of Biomedical and Clinical Sciences 'L. Sacco', University of Milan, Milan, Italy
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17
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Bokharaei-Salim F, Esghaei M, Khanaliha K, Kalantari S, Marjani A, Fakhim A, Keyvani H. HIV-1 reverse transcriptase and protease mutations for drug-resistance detection among treatment-experienced and naïve HIV-infected individuals. PLoS One 2020; 15:e0229275. [PMID: 32119691 PMCID: PMC7051075 DOI: 10.1371/journal.pone.0229275] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/03/2020] [Indexed: 12/03/2022] Open
Abstract
Background The presence of drug resistance mutations (DRMs) against antiretroviral agents is one of the main concerns in the clinical management of individuals with human immunodeficiency virus-1 (HIV-1) infection, especially in regions of the world where treatment options are limited. The current study aimed at assessing the prevalence of HIV-1 DRMs among naïve and treatment-experienced HIV-1-infected patients in Iran. Methods From April 2013 to September 2018, the HIV-1 protease and reverse transcriptase genes were amplified and sequenced in plasma specimens of 60 newly diagnosed antiretroviral-naive individuals and 46 participants receiving antiretroviral therapies (ARTs) for at least six months with an HIV viral load of more than 1000 IU/mL to determine the HIV-1 DRMs and subtypes. Results Among the 60 treatment-naïve HIV-1-infected participants, 8.3% were infected with HIV-1 variants with surveillance DRMs (SDRMs). The SDRMs, D67N and D67E, belonged to the NRTIs class in two patients and K103N and V106A belonged to the NNRTIs class in three patients. The phylogenetic analysis showed that 91.7% of the subjects were infected with subtype CRF35_AD, followed by subtype B (5.0%) and CRF01_AE (3.3%). Among the 46 ART-experienced participants, 33 (71.7%) carried HIV-1 variants with SDRMs (9.1% against PIs, 78.8% against NRTIs, and 100% against NNRTIs). M46I and I47V were the most common mutations for PIs, M184V was the most common mutation for the NRTIs, and K103N/S was the most common mutation for NNRTIs. Phylogenetic analysis of the polymerase region showed that all of the 46 HIV-1-infected patients who failed on ART carried CRF35_AD. Conclusions The moderate prevalence of SDRMs (8.3%) in treatment-naïve and ART-failed (77.1%) Iranian patients with HIV-1-infection emphasizes the need for systematic viral load monitoring, expanding drug resistance testing, carefully surveilling individuals on ART regimens, and facilitating access to new antiretrovirals by health authorities.
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Affiliation(s)
- Farah Bokharaei-Salim
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- * E-mail: ,
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Kalantari
- Departments of Infectious Diseases and Tropical Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Arezoo Marjani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Atousa Fakhim
- Department of Architectural Engineering, Faculty of Engineering, Islamic Azad University, South Tehran Branch, Tehran, Iran
| | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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18
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Günthard HF, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Jacobsen DM, Richman DD. Human Immunodeficiency Virus Drug Resistance: 2018 Recommendations of the International Antiviral Society-USA Panel. Clin Infect Dis 2020; 68:177-187. [PMID: 30052811 PMCID: PMC6321850 DOI: 10.1093/cid/ciy463] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/28/2018] [Indexed: 12/16/2022] Open
Abstract
Background Contemporary antiretroviral therapies (ART) and management strategies have diminished both human immunodeficiency virus (HIV) treatment failure and the acquired resistance to drugs in resource-rich regions, but transmission of drug-resistant viruses has not similarly decreased. In low- and middle-income regions, ART roll-out has improved outcomes, but has resulted in increasing acquired and transmitted resistances. Our objective was to review resistance to ART drugs and methods to detect it, and to provide updated recommendations for testing and monitoring for drug resistance in HIV-infected individuals. Methods A volunteer panel of experts appointed by the International Antiviral (formerly AIDS) Society–USA reviewed relevant peer-reviewed data that were published or presented at scientific conferences. Recommendations were rated according to the strength of the recommendation and quality of the evidence, and reached by full panel consensus. Results Resistance testing remains a cornerstone of ART. It is recommended in newly-diagnosed individuals and in patients in whom ART has failed. Testing for transmitted integrase strand-transfer inhibitor resistance is currently not recommended, but this may change as more resistance emerges with widespread use. Sanger-based and next-generation sequencing approaches are each suited for genotypic testing. Testing for minority variants harboring drug resistance may only be considered if treatments depend on a first-generation nonnucleoside analogue reverse transcriptase inhibitor. Different HIV-1 subtypes do not need special considerations regarding resistance testing. Conclusions Testing for HIV drug resistance in drug-naive individuals and in patients in whom antiretroviral drugs are failing, and the appreciation of the role of testing, are crucial to the prevention and management of failure of ART.
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Affiliation(s)
- Huldrych F Günthard
- University Hospital Zürich and Institute of Medical Virology, University of Zurich, Switzerland
| | - Vincent Calvez
- Pierre et Marie Curie University and Pitié-Salpêtriere Hospital, Paris, France
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute, Hospital Universitari Germans Trias i Pujol, Badalona, Spain.,Africa Health Research Institute, KwaZulu Natal, South Africa
| | | | | | | | | | - Douglas D Richman
- Veterans Affairs San Diego Healthcare System and University of California San Diego
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19
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Soulie C, Santoro MM, Storto A, Abdi B, Charpentier C, Armenia D, Jary A, Forbici F, Bertoli A, Gennari W, Andreoni M, Mussini C, Antinori A, Perno CF, Calvez V, Ceccherini-Silberstein F, Descamps D, Marcelin AG. Prevalence of doravirine-associated resistance mutations in HIV-1-infected antiretroviral-experienced patients from two large databases in France and Italy. J Antimicrob Chemother 2020; 75:1026-1030. [DOI: 10.1093/jac/dkz553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/25/2019] [Accepted: 12/11/2019] [Indexed: 12/20/2022] Open
Abstract
Abstract
Objectives
Doravirine, a novel NNRTI, selects for specific mutations in vitro, including mutations at reverse transcriptase (RT) positions 106, 108, 188, 227, 230 and 234. The aim of this study was to examine the prevalence of doravirine-associated resistance mutations in HIV-1-infected antiretroviral-experienced patients.
Methods
Doravirine-associated resistance mutations identified in vitro or in vivo were studied in a set of 9199 HIV-1 RT sequences from HIV-1 antiretroviral-experienced patients, including 381 NNRTI-failing patients in France and Italy between 2012 and 2017. The following mutations were considered as resistance mutations: V106A/M, V108I, Y188L, G190S, F227C/L/V, M230I/L, L234I, P236L, K103N + Y181C, K103N + P225H and K103N + L100I.
Results
The frequencies of doravirine-associated resistance mutations (total dataset versus NNRTI-failing patients) were: V106A/M, 0.8% versus 2.6%; V108I, 3.3% versus 9.2%; Y188L, 1.2% versus 2.6%; G190S, 0.3% versus 2.1%; F227C/L/V, 0.5% versus 1.8%; M230I/L, 2.8% versus 0%; L234I, 0.1% versus 0.5%; K103N + Y181C, 3.9% versus 3.9%; K103N + P225H, 2.9% versus 4.7%; and K103N + L100I, 1.7% versus 3.9%, with a significantly higher proportion of these mutations in the NNRTI-failing group (P < 0.05), except for M230I/L and K103N + Y181C. The overall prevalence of sequences with at least one doravirine-associated resistance mutation was 12.2% and 34.9% in the total dataset and NNRTI-failing patients (P < 0.001), respectively. In comparison, the prevalence of the common NNRTI mutations V90I, K101E/P, K103N/S, E138A/G/K/Q/R/S, Y181C/I/V and G190A/E/S/Q were higher (8.9%, 7.9%, 28.6%, 12.6%, 14.2% and 8.9%, respectively).
Conclusions
These results suggest that doravirine resistance in antiretroviral-experienced patients generally and specifically among NNRTI-failing patients is lower than resistance to other NNRTIs currently used, confirming its distinguishing resistance pattern.
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Affiliation(s)
- Cathia Soulie
- Sorbonne Université, INSERM, UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | | | - Alexandre Storto
- Université de Paris, INSERM, UMR 1137 IAME, F-75018 Paris, France
| | - Basma Abdi
- Sorbonne Université, INSERM, UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Charlotte Charpentier
- Université de Paris, INSERM, UMR 1137 IAME, F-75018 Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Daniele Armenia
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Aude Jary
- Sorbonne Université, INSERM, UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | - Federica Forbici
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - William Gennari
- Clinic of Infectious Diseases, Modena University Hospital, Modena, Italy
| | - Massimo Andreoni
- Department of Clinical Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, Modena University Hospital, Modena, Italy
| | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Vincent Calvez
- Sorbonne Université, INSERM, UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
| | | | - Diane Descamps
- Université de Paris, INSERM, UMR 1137 IAME, F-75018 Paris, France
- Laboratoire de Virologie, AP-HP, Hôpital Bichat-Claude Bernard, F-75018 Paris, France
| | - Anne-Genevieve Marcelin
- Sorbonne Université, INSERM, UMR_S 1136 Pierre Louis Institute of Epidemiology and Public Health, AP-HP, Hôpital Pitié Salpêtrière, Laboratoire de Virologie, Paris, France
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20
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Al-Omairi O, Elgalib A, Al Kindi H. HIV Drug Resistance among Patients Failing Therapy at a Tertiary Center in Oman: A Case Record Review. Oman Med J 2019; 34:490-495. [PMID: 31745412 PMCID: PMC6851064 DOI: 10.5001/omj.2019.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objectives We sought to estimate the prevalence of HIV drug resistance and describe the common HIV genetic mutations in patients failing antiretroviral therapy (ART). We also investigated the impact of HIV resistance tests results on patients’ management. Methods We conducted a retrospective record review for all HIV genotypic resistance tests requested at the HIV clinic of a tertiary HIV center in Muscat, Oman, from April 2011 to May 2017. Results A total of 98 genotypic resistance tests for 84 patients failing ART were analyzed; 82 tests for 69 patients (83.7%, 95% confidence interval: 76.4–91.0) showed resistance to at least one ART drug. M184V/I, K103N/S, and G190A/S/E were the most common mutations detected. Among the tests with a resistant virus, 78.0% were followed by switching ART based on the resistance test profile resulting in virus load suppression after six months in 60.9% of the cases. Conclusions HIV drug resistance is very common among HIV patients failing ART in Oman, and should be considered in those patients. Switching ART treatment based on the resistance test result leads to a good virological response in adherent patients.
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Affiliation(s)
- Omaira Al-Omairi
- Microbiology Residency Program, Oman Medical Specialty Board, Muscat, Oman
| | - Ali Elgalib
- HIV Clinic, Al Nahdha Hospital, Muscat, Oman.,Directorate General for Disease Surveillance and Control, Ministry of Health, Muscat, Oman
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21
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Boukli N, Boyd A, Collot M, Meynard JL, Girard PM, Morand-Joubert L. Utility of HIV-1 DNA genotype in determining antiretroviral resistance in patients with low or undetectable HIV RNA viral loads. J Antimicrob Chemother 2019; 73:3129-3136. [PMID: 30137336 DOI: 10.1093/jac/dky316] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/09/2018] [Indexed: 01/20/2023] Open
Abstract
Objectives To investigate the extent to which drug resistance can be evaluated from proviral HIV-1 DNA genotype compared with RNA genotype at different timepoints. Patients and methods In HIV-1-infected patients routinely seen at a university hospital, who needed to change their current ART, antiretroviral drug resistance was determined from DNA genotype and was compared with past RNA genotype (group 1) or same-day RNA genotype (group 2). A 'resistance sum' was defined as the sum of agents to which resistance was present and was calculated across NRTI, NNRTI and PI. We defined 'loss of information' as when a lower resistance sum was observed in DNA than in RNA samples. Results Of the 74 and 26 patients included in groups 1 and 2, respectively, most had a long median duration of known HIV-1 infection (17.4 and 14.2 years) and ART (15.3 years and 13.5 years). For group 1, the median (range) resistance sums between DNA/RNA were 0 (0-6)/1 (0-6) for NRTIs, 0 (0-4)/0 (0-4) for NNRTIs and 0 (0-7)/0 (0-8) for PIs, which were comparable with group 2. Loss of information in DNA was substantial for group 1 (37.8%) and less so for group 2 (11.1%). In multivariable analysis, only longer ART duration was significantly associated with loss of information. Results were similar in patients harbouring resistance to one or more agents. Conclusions In a real-life setting, genotyping DNA from PBMC has some degree of concordance compared with RNA. Loss of information in DNA would appear to coincide with longer periods of ART.
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Affiliation(s)
- Narjis Boukli
- AP-HP, Centre Hospitalo-Universitaire Saint-Antoine, Laboratoire de Virologie, Paris, France
| | - Anders Boyd
- INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Marianne Collot
- AP-HP, Centre Hospitalo-Universitaire Saint-Antoine, Laboratoire de Virologie, Paris, France
| | - Jean-Luc Meynard
- AP-HP, Centre Hospitalo-Universitaire Saint-Antoine, Service de Maladies Infectieuses, Paris, France
| | - Pierre-Marie Girard
- AP-HP, Centre Hospitalo-Universitaire Saint-Antoine, Service de Maladies Infectieuses, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
| | - Laurence Morand-Joubert
- AP-HP, Centre Hospitalo-Universitaire Saint-Antoine, Laboratoire de Virologie, Paris, France.,Sorbonne Universités, UPMC Université Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France
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22
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HIV-1 Drug Resistance Among Ugandan Adults Attending an Urban Out-Patient Clinic. J Acquir Immune Defic Syndr 2019; 78:566-573. [PMID: 29771783 DOI: 10.1097/qai.0000000000001717] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Little is known about prevalence of drug resistance among HIV-infected Ugandans, a setting with over 15 years of public sector access to antiretroviral therapy (ART) and where virological monitoring was only recently introduced. SETTING This study was conducted in the adults' out-patient clinic of the Infectious Diseases Institute, Kampala, Uganda. METHODS HIV genotyping was performed in ART-naive patients and in treatment-experienced patients on ART for ≥6 months with virological failure (≥1000 copies/mL). RESULTS A total of 152 ART-naive and 2430 ART-experienced patients were included. Transmitted drug resistance was detected in 9 (5.9%) patients. After a median time on ART of 4.7 years [interquartile range: 2.5-8.7], 190 patients (7.8%) had virological failure with a median viral load of 4.4 log10 copies per milliliter (interquartile range: 3.9-4.9). In addition, 146 patients had a viral load between 51 and 999 copies per milliliter. Most patients with virological failure (142, 74.7%) were on first-line ART. For 163 (85.8%) ART-experienced patients, genotype results were available. Relevant drug-resistance mutations were observed in 135 (82.8%), of which 103 (63.2%) had resistance to 2 drug classes, and 11 (6.7%) had resistance to all drug classes available in Uganda. CONCLUSION The prevalence of transmitted drug resistance was lower than recently reported by the WHO. With 92% of all patients virologically suppressed on ART, the prevalence of virological failure was low when a cutoff of 1000 copies per milliliter is applied, and is in line with the third of the 90-90-90 UNAIDS targets. However, most failing patients had developed multiclass drug resistance.
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23
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Charpentier C, Montes B, Perrier M, Meftah N, Reynes J. HIV-1 DNA ultra-deep sequencing analysis at initiation of the dual therapy dolutegravir + lamivudine in the maintenance DOLULAM pilot study. J Antimicrob Chemother 2018; 72:2831-2836. [PMID: 29091218 DOI: 10.1093/jac/dkx233] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 06/09/2017] [Indexed: 12/12/2022] Open
Abstract
Background The DOLULAM study assessed the efficacy of dolutegravir + lamivudine dual therapy to maintain virological suppression in heavily treatment-experienced HIV-1-infected adults. No virological failure occurred during the first year of the dual therapy. Objectives A virological substudy was conducted to assess the prevalence of M184I/V mutations at dual therapy initiation using historical DNA/RNA genotypes and baseline DNA genotype obtained by next-generation sequencing (NGS). Methods HIV-1 RT sequences were obtained from DNA and/or historical RNA using Sanger technology. HIV-1 DNA RT and integrase NGS was performed using Illumina® technology. Results Among the 27 patients enrolled in the DOLULAM study, historical HIV DNA and RNA Sanger sequences were available in 14 and 18 patients, respectively. At the initiation of DOLULAM, DNA NGS genotypes showed that 45% and 21% of the patients harboured minority resistant variants (MRV) in RT and integrase, respectively. Combining all available genotype data, an M184I/V was observed in 17 of 27 (63%) of the patients. Most M184V were detected in historical RNA genotypes (n = 8 of 11), whereas M184I were exclusively detected in DNA genotypes (n = 10, including 7 as MRV). Ten patients displayed defective viral genomes in cellular reservoirs, all including M184I and stop codons. At the time of DOLULAM initiation, M184V was observed in DNA NGS in five patients, including one as MRV. Conclusions These first NGS data on HIV DNA at initiation of a switch study showed (i) a high proportion of patients harbouring defective viral genomes, whose mutation M184I is a marker, and (ii) a low number of patients in whom M184V remained as a major viral variant in PBMCs.
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Affiliation(s)
- Charlotte Charpentier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Brigitte Montes
- Laboratoire de Virologie, CHU de Montpellier, Montpellier, France
| | - Marine Perrier
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France
| | - Nadia Meftah
- COREVIH, CHU de Montpellier, Montpellier, France
| | - Jacques Reynes
- Département de Maladies infectieuses et tropicales, CHU de Montpellier, Montpellier, France.,Unité Mixte Internationale 233 IRD-U1175 INSERM-Université de Montpellier, Montpellier, France
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24
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Matsuda EM, Coelho LPO, de Faria Romero G, Moraes MJD, Lopez-Lopes GIS, Morejon K, Campeas AE, Cabral GB, Brígido LFDM, Salvage Therapy Working Group. High Prevalence of Drug Resistance Mutations Among Patients Failing First-Line Antiretroviral Therapy and Predictors of Virological Response 24 Weeks After Switch to Second-Line Therapy in São Paulo State, Brazil. AIDS Res Hum Retroviruses 2018; 34:156-164. [PMID: 28969448 DOI: 10.1089/aid.2017.0052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Universal antiretroviral treatment with sustained viral suppression benefits patients and reduces HIV transmission. Effectiveness of therapy may be limited by antiretroviral drug resistance. Information on the resistance profile at treatment failure and its impact on antiretroviral drugs may subsidize subsequent treatment strategies. Partial pol sequences from 319 patients failing first-line therapy were analyzed for resistance associated mutations (RAMs) and HIV subtype. Demographic data, CD4 T cell count, viral load, and antiretroviral regimens and mutational profile at first-line failure were also investigated for associations to the response to second-line regimens. RAMs at the reverse transcriptase gene were frequent. Most sequences (88%) showed at least one mutation. A higher number of reverse transcriptase RAMs were associated to lower CD4 T cell counts and the use of tenofovir/lamivudine in first line. Among 205 with follow-up data, 76.6% were virally suppressed (below 200 copies/ml) after 24 weeks of second-line therapy. Most cases initiated second line with a regimen genotypic susceptibility score ≥2, but it did not predict viral suppression, that was independently associated with higher CD4 T cell counts and with the presence of nucleos(t)ide analog reverse transcriptase inhibitor (NRTI) RAMs. This study documented extensive resistance at first-line failure in this area in Brazil, highlights the risks of low CD4 T cell counts to second-line therapy, and supports the notion that recycled NRTIs may contribute to viral suppression even when genotypic resistance is present.
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Affiliation(s)
- Elaine Monteiro Matsuda
- Ambulatório de referência de moléstias infecciosas, Programa de AIDS de Santo André, Santo André, Brazil
| | - Luana Portes Ozório Coelho
- Núcleo de doenças de vinculação sanguínea ou sexual, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, Brazil
| | - Giselle de Faria Romero
- Núcleo de doenças de vinculação sanguínea ou sexual, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, Brazil
| | | | | | - Karen Morejon
- Departamento de Clínica Médica, Hospital das Clínicas, Faculdade de Medicina, Ribeirão Preto, Brazil
| | | | - Gabriela Bastos Cabral
- Núcleo de doenças de vinculação sanguínea ou sexual, Centro de Virologia, Instituto Adolfo Lutz, São Paulo, Brazil
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25
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Raizes E, Hader S, Birx D. Expansion of Viral Load Testing and the Potential Impact on HIV Drug Resistance. J Infect Dis 2017; 216:S805-S807. [PMID: 29206999 DOI: 10.1093/infdis/jix432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The US President's Emergency Plan for AIDS Relief (PEPFAR) supports aggressive scale-up of antiretroviral therapy (ART) in high-burden countries and across all genders and populations at risk toward global human immunodeficiency virus (HIV) epidemic control. PEPFAR recognizes the risk of HIV drug resistance (HIVDR) as a consequence of aggressive ART scale-up and is actively promoting 3 key steps to mitigate the impact of HIVDR: (1) routine access to routine viral load monitoring in all settings; (2) optimization of ART regimens; and (3) routine collection and analysis of HIVDR data to monitor the success of mitigation strategies. The transition to dolutegravir-based regimens in PEPFAR-supported countries and the continuous evolution of HIVDR surveillance strategies are essential elements of PEPFAR implementation.
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Affiliation(s)
- Elliot Raizes
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention
| | - Shannon Hader
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention
| | - Deborah Birx
- Office of the US Global AIDS Coordinator, US Department of State
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