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Fabeni L, Armenia D, Abbate I, Gagliardini R, Mazzotta V, Bertoli A, Gennari W, Forbici F, Berno G, Piermatteo L, Borghi V, Pinnetti C, Vergori A, Mondi A, Parruti G, Di Sora F, Iannetta M, Lichtner M, Latini A, Mussini C, Sarmati L, Perno CF, Girardi E, Antinori A, Ceccherini-Silberstein F, Maggi F, Santoro MM. HIV-1 transmitted drug resistance in newly diagnosed individuals in Italy over the period 2015-21. J Antimicrob Chemother 2024:dkae189. [PMID: 39028674 DOI: 10.1093/jac/dkae189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/22/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Transmitted drug resistance (TDR) is still a critical aspect for the management of individuals living with HIV-1. Thus, its evaluation is crucial to optimize HIV care. METHODS Overall, 2386 HIV-1 protease/reverse transcriptase and 1831 integrase sequences from drug-naïve individuals diagnosed in north and central Italy between 2015 and 2021 were analysed. TDR was evaluated over time. Phylogeny was generated by maximum likelihood. Factors associated with TDR were evaluated by logistic regression. RESULTS Individuals were mainly male (79.1%) and Italian (56.2%), with a median (IQR) age of 38 (30-48). Non-B infected individuals accounted for 44.6% (N = 1065) of the overall population and increased over time (2015-2021, from 42.1% to 51.0%, P = 0.002). TDR prevalence to any class was 8.0% (B subtype 9.5% versus non-B subtypes 6.1%, P = 0.002) and remained almost constant over time. Overall, 300 transmission clusters (TCs) involving 1155 (48.4%) individuals were identified, with a similar proportion in B and non-infected individuals (49.7% versus 46.8%, P = 0.148). A similar prevalence of TDR among individuals in TCs and those out of TCs was found (8.2% versus 7.8%, P = 0.707).By multivariable analysis, subtypes A, F, and CFR02_AG were negatively associated with TDR. No other factors, including being part of TCs, were significantly associated with TDR. CONCLUSIONS Between 2015 and 2021, TDR prevalence in Italy was 8% and remained almost stable over time. Resistant strains were found circulating regardless of being in TCs, but less likely in non-B subtypes. These results highlight the importance of a continuous surveillance of newly diagnosed individuals for evidence of TDR to inform clinical practice.
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Affiliation(s)
- Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Daniele Armenia
- Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Isabella Abbate
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Roberta Gagliardini
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Ada Bertoli
- Laboratory of Virology, Department of Laboratory Medicine, University Hospital Tor Vergata, Rome, Italy
| | - William Gennari
- Molecular Microbiology and Virology Unit, Department of Laboratory Medicine and Pathological Anatomy, Policlinic of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giulia Berno
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Vanni Borghi
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Carmela Pinnetti
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Alessandra Vergori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Annalisa Mondi
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Giustino Parruti
- Infectious Diseases Unit, Pescara General Hospital, Pescara, Italy
| | - Fiorella Di Sora
- Unit of Clinical Immunology, San Giovanni Addolorata Hospital, Rome, Italy
| | - Marco Iannetta
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Miriam Lichtner
- Infectious Diseases Unit, Santa Maria Goretti Hospital, Sapienza University of Rome, Polo Pontino, Latina, Italy
- Sant'Andrea Hospital, Clinical Infectious Diseases, Rome, Italy
| | - Alessandra Latini
- Sexually Transmitted Infection/Human Immunodeficiency Virus Unit, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Cristina Mussini
- Department of Infectious Diseases, Azienda Ospedaliero-Universitaria, Policlinico of Modena, Modena, Italy
| | - Loredana Sarmati
- Department of Infectious Diseases, University Hospital Tor Vergata, Rome, Italy
| | - Carlo Federico Perno
- Microbiology and Diagnostic Immunology Unit, Department of Diagnostic and Laboratory Medicine, Bambino Gesú Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Girardi
- Scientific Direction, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | - Andrea Antinori
- Clinical and Research Infectious Diseases Department, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
| | | | - Fabrizio Maggi
- Laboratory of Virology, National Institute for Infectious Diseases, Lazzaro Spallanzani IRCCS, Rome, Italy
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Fofana DB, Diarra H, Guindo I, Savadogo MK, d’Almeida M, Diallo FI, Baldé A, Soulié C, Kone A, Marcelin AG, Maiga AI, Lambert-Niclot S, Maiga M, McFall S, Hawkins CA, Murphy RL, Sylla M, Katlama C, Holl JL, Calvez V, Morand-Joubert L. Prevalence of HIV-1 Natural Polymorphisms and Integrase-Resistance-Associated Mutations in African Children. Viruses 2023; 15:v15020546. [PMID: 36851760 PMCID: PMC9964382 DOI: 10.3390/v15020546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/05/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023] Open
Abstract
Integrase inhibitors (INIs) are a potent option for HIV treatment. Limited data exist on INI resistance in West Africa, particularly in children living with HIV/AIDS. We determined the prevalence of integrase gene polymorphisms and the frequency of naturally occurring amino acid (aa) substitutions at positions associated with INI resistance. Dried blood spot (DBS) samples were obtained from one hundred and seven (107) HIV-1-infected children aged less than 15 years old in two West African countries, Benin and Mali. All children were naïve to INI treatment, 56 were naïve to anti-retroviral therapy (ART), and 51 had received ART. Genetic sequencing of HIV integrase was successful in 75 samples. The aa changes at integrase positions associated with INI resistance were examined according to the Stanford HIV Genotypic Resistance database. The median ages were 2.6 and 10 years for ART-naïve and -treated children, respectively. The most common subtypes observed were CRF02_AG (74.7%) followed by CRF06_cpx (20%). No major INI-resistance mutations at positions 66, 92, 121, 143, 147, 148, 155, and 263 were detected. The most prevalent INI accessory resistance mutations were: L74I/M (14/75, 18.6%) followed by E157Q (8/75, 10.6%), G163E/N/T/Q (5/75, 6.6%), Q95A/H/P (2/75, 2.6%), and T97A (4/75, 5.3%). Other substitutions observed were M50I/L/P, H51E/P/S/Q, I72V, T112V, V201I, and T206S. Polymorphisms at positions which may influence the genetic barrier and/or drive the selection of specific INI-resistance pathways were detected. However, no transmitted drug resistance (TDR) to INI was detected among samples of INI-naïve patients. These findings support the use of this treatment class for children with HIV-1, particularly in West Africa.
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Affiliation(s)
- Djeneba B. Fofana
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
- Correspondence:
| | - Houdou Diarra
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Ibrahima Guindo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | | | - Marceline d’Almeida
- Département Mère Enfant, Faculté Des Sciences De La Santé, Université Abomey-Calavi, CNHU—HKM, Cotonou 229, Benin
| | - Fatoumata I. Diallo
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Aliou Baldé
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
| | - Cathia Soulié
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Amadou Kone
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Almoustapha I. Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Sidonie Lambert-Niclot
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
| | - Mamoudou Maiga
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Sally McFall
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Claudia A. Hawkins
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Robert L. Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60208, USA
| | - Mariam Sylla
- Faculty of Medicine, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako E 423, Mali
| | - Christine Katlama
- Service des Maladies Infectieuses, Hôpital Pitié-Salpêtrière APHP, F-75013 Paris, France
| | - Jane L. Holl
- Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-HÔpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, F-75013 Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), F-75012 Paris, France
- Department of Virology, Assistance Publique-Hôpitaux de Paris (AP-HP), Saint-Antoine Hospital, F-75012 Paris, France
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Chu C, Armenia D, Walworth C, Santoro MM, Shafer RW. Genotypic Resistance Testing of HIV-1 DNA in Peripheral Blood Mononuclear Cells. Clin Microbiol Rev 2022; 35:e0005222. [PMID: 36102816 PMCID: PMC9769561 DOI: 10.1128/cmr.00052-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HIV-1 DNA exists in nonintegrated linear and circular episomal forms and as integrated proviruses. In patients with plasma viremia, most peripheral blood mononuclear cell (PBMC) HIV-1 DNA consists of recently produced nonintegrated virus DNA while in patients with prolonged virological suppression (VS) on antiretroviral therapy (ART), most PBMC HIV-1 DNA consists of proviral DNA produced months to years earlier. Drug-resistance mutations (DRMs) in PBMCs are more likely to coexist with ancestral wild-type virus populations than they are in plasma, explaining why next-generation sequencing is particularly useful for the detection of PBMC-associated DRMs. In patients with ongoing high levels of active virus replication, the DRMs detected in PBMCs and in plasma are usually highly concordant. However, in patients with lower levels of virus replication, it may take several months for plasma virus DRMs to reach detectable levels in PBMCs. This time lag explains why, in patients with VS, PBMC genotypic resistance testing (GRT) is less sensitive than historical plasma virus GRT, if previous episodes of virological failure and emergent DRMs were either not prolonged or not associated with high levels of plasma viremia. Despite the increasing use of PBMC GRT in patients with VS, few studies have examined the predictive value of DRMs on the response to a simplified ART regimen. In this review, we summarize what is known about PBMC HIV-1 DNA dynamics, particularly in patients with suppressed plasma viremia, the methods used for PBMC HIV-1 GRT, and the scenarios in which PBMC GRT has been used clinically.
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Affiliation(s)
- Carolyn Chu
- Department of Family and Community Medicine, University of California San Francisco, San Francisco, California, USA
| | - Daniele Armenia
- UniCamillus, Saint Camillus International University of Health Sciences, Rome, Italy
| | - Charles Walworth
- LabCorp-Monogram Biosciences, South San Francisco, California, USA
| | - Maria M. Santoro
- Department of Experimental Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Robert W. Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
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Armenia D, Forbici F, Bertoli A, Berno G, Malagnino V, Gagliardini R, Borghi V, Gennari W, Cicalini S, Buonomini A, Teti E, Lanini S, Latini A, Sarmati L, Mussini C, Andreoni M, Antinori A, Perno C, Ceccherini-Silberstein F, Santoro M. Bictegravir/emtricitabine/tenofovir alafenamide ensures high rates of virological suppression maintenance despite previous resistance in PLWH who optimize treatment in clinical practice. J Glob Antimicrob Resist 2022; 30:326-334. [DOI: 10.1016/j.jgar.2022.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/12/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022] Open
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Vergni D, Santoni D, Bouba Y, Lemme S, Fabeni L, Carioti L, Bertoli A, Gennari W, Forbici F, Perno CF, Gagliardini R, Ceccherini-Silberstein F, Santoro MM. Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105294. [PMID: 35513162 DOI: 10.1016/j.meegid.2022.105294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/24/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
This study aimed at updating previous data on HIV-1 integrase variability, by using effective bioinformatics methods combining different statistical instruments from simple entropy and mutation rate to more specific approaches such as Hellinger distance. A total of 2133 HIV-1 integrase sequences were analyzed in: i) 1460 samples from drug-naïve [DN] individuals; ii) 386 samples from drug-experienced but INI-naïve [IN] individuals; iii) 287 samples from INI-experienced [IE] individuals. Within the three groups, 76 amino acid positions were highly conserved (≤0.2% variation, Hellinger distance: <0.25%), with 35 fully invariant positions; while, 80 positions were conserved (>0.2% to <1% variation, Hellinger distance: <1%). The H12-H16-C40-C43 and D64-D116-E152 motifs were all well conserved. Some residues were affected by dramatic changes in their mutation distributions, especially between DN and IE samples (Hellinger distance ≥1%). In particular, 15 positions (D6, S24, V31, S39, L74, A91, S119, T122, T124, T125, V126, K160, N222, S230, C280) showed a significant decrease of mutation rate in IN and/or IE samples compared to DN samples. Conversely, 8 positions showed significantly higher mutation rate in samples from treated individuals (IN and/or IE) compared to DN. Some of these positions, such as E92, T97, G140, Y143, Q148 and N155, were already known to be associated with resistance to integrase inhibitors; other positions including S24, M154, V165 and D270 are not yet documented to be associated with resistance. Our study confirms the high conservation of HIV-1 integrase and identified highly invariant positions using robust and innovative methods. The role of novel mutations located in the critical region of HIV-1 integrase deserves further investigation.
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Affiliation(s)
- Davide Vergni
- Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR, Rome, Italy.
| | - Daniele Santoni
- Istituto di Analisi dei Sistemi ed. Informatica "Antonio Ruberti" - CNR, Rome, Italy
| | - Yagai Bouba
- Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management (CIRCB), Yaoundé, Cameroon; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Saverio Lemme
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; Laboratory of Virology, University Hospital "Tor Vergata", Rome, Italy
| | - William Gennari
- Microbiology and Virology Unit, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Forbici
- Laboratory of Virology, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
| | - Carlo Federico Perno
- Multimodal Laboratory Research Department, Children Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Roberta Gagliardini
- HIV/AIDS Department, IRCCS, National Institute for Infectious Diseases "Lazzaro Spallanzani", Rome, Italy
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Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience. Int J Mol Sci 2022; 23:ijms23052727. [PMID: 35269868 PMCID: PMC8911269 DOI: 10.3390/ijms23052727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/22/2023] Open
Abstract
Drug-resistance monitoring is one of the hardest challenges in HIV management. Next-generation sequencing (NGS) technologies speed up the detection of drug resistance, allowing the adjustment of antiretroviral therapy and enhancing the quality of life of people living with HIV. Recently, the NGS Sentosa® SQ HIV Genotyping Assay (Vela Diagnostics) received approval for in vitro diagnostics use. This work is the first Italian evaluation of the performance of the Vela Diagnostics NGS platform, assessed with 420 HIV-1 clinical samples. A comparison with Sanger sequencing performance is also reported, highlighting the advantages and disadvantages of the Sentosa® NGS assay. The precision of the technology was studied with reference specimens, while intra- and inter-assay reproducibility were evaluated for selected clinical samples. Vela Diagnostics’ NGS assay reached an 87% success rate through 30 runs of analysis in a real-world clinical context. The concordance with Sanger sequencing outcomes was equal to 97.2%. Several detected mismatches were due to NGS’s superior sensitivity to low-frequency variants. A high accuracy was observed in testing reference samples. Repeatability and reproducibility assays highlighted the good performance of the NGS platform. Beyond a few technical issues that call for further optimization, the key improvement will be a better balance between costs and processing speed. Once these issues have been solved, the Sentosa® SQ HIV Genotyping Assay will be the way forward for HIV resistance testing.
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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Armenia D, Bouba Y, Gagliardini R, Gori C, Bertoli A, Borghi V, Gennari W, Micheli V, Callegaro AP, Gazzola L, Bruzzone B, Giannetti A, Mazzotta V, Vergori A, Mastrorosa I, Colafigli M, Lichtner M, di Biagio A, Maggiolo F, Rizzardini G, d'Arminio Monforte A, Andreoni M, Mussini C, Antinori A, Ceccherini-Silberstein F, Perno CF, Santoro MM. Evaluation of virological response and resistance profile in HIV-1 infected patients starting a first-line integrase inhibitor-based regimen in clinical settings. J Clin Virol 2020; 130:104534. [PMID: 32769022 DOI: 10.1016/j.jcv.2020.104534] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/05/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Virological response and resistance profile were evaluated in drug-naïve patients starting their first-line integrase inhibitors (INIs)-based regimen in a clinical setting. STUDY DESIGN Virological success (VS) and virological rebound (VR) after therapy start were assessed by survival analyses. Drug-resistance was evaluated at baseline and at virological failure. RESULTS Among 798 patients analysed, 38.6 %, 27.1 % and 34.3 % received raltegravir, elvitegravir and dolutegravir, respectively. Baseline resistance to NRTIs, NNRTIs, PIs and INIs was: 3.9 %, 13.9 %, 1.6 % and 0.5 %, respectively. Overall, by 12 months of treatment, the probability of VS was 95 %, while the probability of VR by 36 months after VS was 13.1 %. No significant differences in the virological response were found according to the INI used. The higher pre-therapy viremia strata was (<100,000 vs. 100,000-500,000 vs. > 500,000 copies/mL), lower was the probability of VS (96.0 % vs. 95.2 % vs. 91.1 %, respectively, P < 0.001), and higher the probability of VR (10.2 % vs. 15.8 % vs. 16.6 %, respectively, P = 0.010). CD4 cell count <200 cell/mm3 was associated with the lowest probability of VS (91.5 %, P < 0.001) and the highest probability of VR (20.7 %, P = 0.008) compared to higher CD4 levels. Multivariable Cox-regression confirmed the negative role of high pre-therapy viremia and low CD4 cell count on VS, but not on VR. Forty-three (5.3 %) patients experienced VF (raltegravir: 30; elvitegravir: 9; dolutegravir: 4). Patients failing dolutegravir did not harbor any resistance mutation either in integrase or reverse transcriptase. CONCLUSIONS Our findings confirm that patients receiving an INI-based first-line regimen achieve and maintain very high rates of VS in clinical practice.
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Affiliation(s)
- Daniele Armenia
- Saint Camillus International University of Health and Medical Sciences, Rome, Italy
| | - Yagai Bouba
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Roberta Gagliardini
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Caterina Gori
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Vanni Borghi
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - William Gennari
- Microbiology and Virology Unit, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Valeria Micheli
- Department of Clinical Microbiology, Virology and Diagnosis of Bioemergency, Luigi Sacco University Hospital, Milano, Italy
| | | | - Lidia Gazzola
- Department of Health Sciences, Clinic of Infectious Diseases, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | - Bianca Bruzzone
- Hygiene Unit, Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Giannetti
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Valentina Mazzotta
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Alessandra Vergori
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Ilaria Mastrorosa
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | - Manuela Colafigli
- Unit of Dermatology and Sexually Transmitted Diseases, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Miriam Lichtner
- Infectious Diseases Unit, "Sapienza" University, Polo Pontino, Latina, Italy
| | - Antonio di Biagio
- Infectious Diseases Clinic, Policlinico San Martino Hospital, Department of Health Sciences (DISSAL), University of Genoa, Genova, Italy
| | - Franco Maggiolo
- Division of Infectious Diseases, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Giuliano Rizzardini
- Department of Infectious Diseases, Luigi Sacco University Hospital, Milano, Italy
| | - Antonella d'Arminio Monforte
- Department of Health Sciences, Clinic of Infectious Diseases, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | - Massimo Andreoni
- Clinical Infectious Diseases, University Hospital "Tor Vergata", Rome, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Antinori
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases "Lazzaro Spallanzani", IRCCS, Rome, Italy
| | | | - Carlo Federico Perno
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
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9
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Armenia D, Di Carlo D, Cozzi-Lepri A, Calcagno A, Borghi V, Gori C, Bertoli A, Gennari W, Bellagamba R, Castagna A, Latini A, Pinnetti C, Cicalini S, Saracino A, Lapadula G, Rusconi S, Castelli F, Di Giambenedetto S, Andreoni M, Di Perri G, Antinori A, Mussini C, Ceccherini-Silberstein F, Monforte AD, Perno CF, Santoro MM. Very high pre-therapy viral load is a predictor of virological rebound in HIV-1-infected patients starting a modern first-line regimen. Antivir Ther 2020; 24:321-331. [PMID: 30977466 DOI: 10.3851/imp3309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Pre-cART (combined antiretroviral therapy) plasma viral load >500,000 copies/ml has been associated with a lower probability of achieving virological suppression, while few data about its role on maintenance of virological suppression are available. In this study we aimed to clarify whether high levels of pre-cART viraemia are associated with virological rebound (VR) after virological suppression. METHODS HIV-infected individuals who achieved virological suppression after first-line cART were included. VR was defined as the first of two consecutive viraemia >50 copies/ml (VR50) or, in an alternative analysis, >200 copies/ml (VR200). The impact of pre-cART viraemia on the risk of VR was evaluated by survival analyses. RESULTS Among 5,766 patients included, 59.2%, 31.4%, 5.2% and 4.2% had pre-cART viraemia ≤100,000, 100,001-500,000, 500,001-1,000,000 and >1,000,000 copies/ml, respectively. Patients with pre-cART viraemia levels >1,000,000 copies/ml had the highest probability of VR (>1,000,000; 500,000-1,000,000; 100,000-500,000; <100,000 copies/ml; VR50: 28.4%; 24.3%; 17.6%; 13.8%, P<0.0001; VR200: 14.4%; 11.1%; 7.2%; 7.6%; P=0.009). By Cox multivariable analyses, patients with pre-cART viraemia >500,000 and >1,000,000 copies/ml showed a significantly higher risk of VR regardless of the VR end point used. No difference in the risk of VR was found between patients with pre-cART viraemia ranging 500,000-1,000,000 copies/ml and those with pre-cART viraemia >1,000,000 copies/ml, regardless of the VR end point used. CONCLUSIONS Pre-cART plasma viral load levels >500,000 copies/ml can identify fragile patients with poorer chance of maintaining virological control after an initial response. An effort in defining effective treatment strategies is mandatory for these patients that remain difficult to treat.
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Affiliation(s)
- Daniele Armenia
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy.,Saint Camillus International University of Health Sciences, Rome, Italy
| | - Domenico Di Carlo
- Pediatric Clinical Research Center 'Romeo and Erica Invernizzi', University of Milan, Milan, Italy
| | | | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Vanni Borghi
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | - Caterina Gori
- Virology Unit, 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
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Rita Bellagamba
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Antonella Castagna
- Infectious Diseases Department, IRCCS San Raffaele Scientific Institute & Vita-Salute University, Milan, Italy
| | - Alessandra Latini
- Unit of Dermatology and Sexually Transmitted Diseases, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Carmela Pinnetti
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Stefania Cicalini
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Annalisa Saracino
- Division of Infectious Diseases, University of Bari, Policlinic Hospital, Bari, Italy
| | - Giuseppe Lapadula
- Division of Infectious Diseases, 'San Gerardo' Hospital, Monza, Italy
| | - Stefano Rusconi
- Infectious Diseases Unit, DIBIC Luigi Sacco, University of Milan, Milan, Italy
| | - Francesco Castelli
- University Department of Infectious and Tropical Diseases, University of Brescia and Spedali Civili General Hospital, Brescia, Italy
| | | | - Massimo Andreoni
- Clinical Infectious Diseases, University Hospital 'Tor Vergata', Rome, Italy
| | - Giovanni Di Perri
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Andrea Antinori
- Clinical Division of HIV/AIDS, National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University Hospital, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Antonella D'Arminio Monforte
- Department of Health Sciences, Clinic of Infectious Diseases, ASST Santi Paolo e Carlo, University of Milan, Milan, Italy
| | - Carlo F Perno
- Virology Unit, National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Maria M Santoro
- Department of Experimental Medicine, University of Rome 'Tor Vergata', Rome, Italy
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10
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Scutari R, Alteri C, Vicenti I, Di Carlo D, Zuccaro V, Incardona F, Borghi V, Bezenchek A, Andreoni M, Antinori A, Perno CF, Cascio A, De Luca A, Zazzi M, Santoro MM. Evaluation of HIV-1 integrase resistance emergence and evolution in patients treated with integrase inhibitors. J Glob Antimicrob Resist 2019; 20:163-169. [PMID: 31330378 DOI: 10.1016/j.jgar.2019.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/26/2019] [Accepted: 07/12/2019] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVES This study evaluated the emergence of mutations associated with integrase strand transfer inhibitors (INSTI) resistance (INSTI-RMs) and the integrase evolution in human immunodeficiency virus type 1 (HIV-1) infected patients treated with this drug class. METHODS The emergence of INSTI-RMs and integrase evolution (estimated as genetic distance between integrase sequences under INSTI treatment and before INSTI treatment) were evaluated in 107 INSTI-naïve patients (19 drug-naïve and 88 drug-experienced) with two plasma genotypic resistance tests: one before INSTI treatment and one under INSTI treatment. A logistic regression analysis was performed to evaluate factors associated with the integrase evolution under INSTI treatment. RESULTS The patients were mainly infected by B subtype (72.0%). Eighty-seven patients were treated with raltegravir, 13 with dolutegravir and seven with elvitegravir. Before INSTI treatment one patient harboured the major INSTI-RM R263K and three patients the accessory INSTI-RMs T97A. Under INSTI treatment the emergence of ≥1 INSTI-RM was found in 39 (36.4%) patients. The major INSTI-RMs that more frequently emerged were: N155H (17.8%), G140S (8.4%), Y143R (7.5%), Q148H (6.5%), and Y143C (4.7%). Concerning integrase evolution, a higher genetic distance was found in patients with ≥1 INSTI-RM compared with those without emergence of resistance (0.024 [0.012-0.036] vs. 0.015 [0.009-0.024], P=0.018). This higher integrase evolution was significantly associated with a longer duration of HIV-1 infection, a higher number of past regimens and non-B subtypes. CONCLUSIONS These findings confirm that major INSTI-RMs very rarely occur in INSTI-naïve patients. Under INSTI treatment, selection of drug-resistance follows the typical drug-resistance pathways; a higher evolution characterises integrase sequences developing drug-resistance compared with those without any resistance.
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Affiliation(s)
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | | | - Domenico Di Carlo
- University of Milan, Paediatric Clinical Research Center "Romeo and Enrica Invernizzi", Milan, Italy
| | | | | | - Vanni Borghi
- Infectious Diseases Clinics, Azienda Ospedaliero-Universitaria Policlinico di Modena, Modena, Italy
| | | | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
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11
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Modica S, Rossetti B, Lombardi F, Lagi F, Maffeo M, D'Autilia R, Pecorari M, Vicenti I, Bruzzone B, Magnani G, Paolucci S, Francisci D, Penco G, Sacchini D, Zazzi M, De Luca A, Di Biagio A. Prevalence and determinants of resistance mutations in HIV-1-infected patients exposed to integrase inhibitors in a large Italian cohort. HIV Med 2018; 20:137-146. [PMID: 30461149 DOI: 10.1111/hiv.12692] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVES The aim of the study was to analyse the prevalence of integrase resistance mutations in integrase strand transfer inhibitor (INSTI)-experienced HIV-1-infected patients and its predictors. METHODS We selected HIV-1 integrase sequences from the Antiviral Response Cohort Analysis (ARCA) database, derived from INSTI-experienced patients between 2008 and 2017. Differences in the prevalence of resistance to raltegravir (RAL), elvitegravir (EVG) and dolutegravir (DTG) were assessed by χ2 test and predictors of resistance were analysed by logistic regression. RESULTS We included 462 genotypes from INSTI-exposed individuals: 356 'INSTI-failing' patients and 106 'previously INSTI-exposed' patients (obtained a median of 42 weeks after INSTI discontinuation [interquartile range (IQR) 17-110 weeks]). Overall, at least low-level resistance (LLR) to any INSTI (Stanford 8.5 algorithm) was detected in 198 (42.9%) cases. The most frequent INSTI resistance mutation was N155H, followed by Q148H/K/R, G140A/C/S, E138A/K/T and Y143C/H/R. Y143R and E138A were more prevalent in viral subtype B versus non-B [5.2 versus 1.5%, respectively (P = 0.04), and 3.1 versus 0%, respectively (P = 0.02)]. Overall, the Q148H/K/R plus G140A/C/S and/or E138A/K/T pattern, defining an intermediate level of resistance to DTG, was detected in 70 (15%) cases. Independent predictors of at least LLR to any INSTI were current use versus past use of INSTIs, a lower genotypic sensitivity score (GSS) for contemporary antiretroviral drugs used, and having an integrase sequence obtained in calendar year 2016 as compared to 2008-2009. CONCLUSIONS The results support integrase resistance testing in INSTI-experienced patients. Emergence of INSTI resistance is facilitated by the reduced genetic barrier of the regimen as a consequence of resistance to companion drugs. However, INSTI resistance may become undetectable by standard population sequencing upon INSTI discontinuation.
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Affiliation(s)
- S Modica
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - B Rossetti
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy
| | - F Lombardi
- Institute of Clinical Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
| | - F Lagi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - M Maffeo
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - R D'Autilia
- Department of Mathematics, University of Roma Tre, Rome, Italy
| | - M Pecorari
- Unit of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - I Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - B Bruzzone
- Hygiene Unit, Policlinico San Martino Hospital, Genoa, Italy
| | - G Magnani
- Department of Infectious Diseases, S. Maria Nuova IRCCS Hospital, Reggio Emilia, Italy
| | - S Paolucci
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS San Matteo Hospital Foundation, Pavia, Italy
| | - D Francisci
- Infectious Diseases Clinic, Perugia University Hospital, Perugia, Italy
| | - G Penco
- Department of Infectious Diseases, Galliera Hospital, Genoa, Italy
| | - D Sacchini
- Clinic of Infectious Diseases, 'Guglielmo da Saliceto' Hospital, Piacenza, Italy
| | - M Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - A De Luca
- Infectious Diseases Unit, Siena University Hospital, Siena, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - A Di Biagio
- Infectious Diseases Clinic, Policlinico San Martino Hospital, Genoa, Italy
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12
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Marino-Merlo F, Macchi B, Armenia D, Bellocchi MC, Ceccherini-Silberstein F, Mastino A, Grelli S. Focus on recently developed assays for detection of resistance/sensitivity to reverse transcriptase inhibitors. Appl Microbiol Biotechnol 2018; 102:9925-9936. [PMID: 30269214 DOI: 10.1007/s00253-018-9390-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022]
Abstract
The biology of HIV is rather complex due to high rate of replication, frequent recombination, and introduction of mutations. This gives rise to a number of distinct variants referred as quasispecies. In addition, the latency within reservoir allows the periodic reactivation of virus replication. The rapid replication of HIV allows immune response escape and establishment of resistance to therapy that can be acquired through drug selection and/or transmitted among individuals. This prompted, over the years, the development of a range of assays aimed to determine drug resistance and sensitivity, to be used both in clinical practice and in antiviral research. Reverse transcriptase (RT) inhibitors have an eminent place among the anti-HIV drugs, being constantly present from the beginning until today in the most commonly used antiviral regimens. This mini-review seeks to provide an up-to-date overview of recent efforts in developing even more reliable and simple methods, of both genotypic and phenotypic types, for specifically detecting drug resistance and sensitivity to RT inhibitors.
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Affiliation(s)
| | - Beatrice Macchi
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Antonio Mastino
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Via F. Stagno d'Alcontres 31, 98166, Messina, Italy. .,The Institute of Translational Pharmacology, CNR, Rome, Italy.
| | - Sandro Grelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
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13
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Jaffré J, Armenia D, Bellocchi MC, Wirden M, Carioti L, Lambert S, Valantin MA, Nguyen T, Simon A, Katlama C, Andreoni M, Perno CF, Calvez V, Ceccherini-Silberstein F, Marcelin AG, Todesco E. Ultradeep sequencing detection of the R263K integrase inhibitor drug resistance mutation. J Antimicrob Chemother 2018; 72:1537-1539. [PMID: 28088769 DOI: 10.1093/jac/dkw571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jérémy Jaffré
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | - Marc Wirden
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Luca Carioti
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Sidonie Lambert
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Marc-Antoine Valantin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Thuy Nguyen
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Anne Simon
- Department of Internal Medicine, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Christine Katlama
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Massimo Andreoni
- Infectious Diseases, University Hospital of Rome Tor Vergata, Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | | | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
| | - Eve Todesco
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, F75013, France.,Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP, Paris, F75013, France
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14
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Armenia D, Zaccarelli M, Borghi V, Gennari W, Di Carlo D, Giannetti A, Forbici F, Bertoli A, Gori C, Fabeni L, Pinnetti C, Marocco R, Latini A, Ceccherini-Silberstein F, Mastroianni CM, Mussini C, Antinori A, Perno CF, Santoro MM. Resistance detected in PBMCs predicts virological rebound in HIV-1 suppressed patients switching treatment. J Clin Virol 2018; 104:61-64. [PMID: 29738896 DOI: 10.1016/j.jcv.2018.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 04/02/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND Genotypic resistance test (GRT) performed in peripheral blood mononuclear cells (PBMC) represents a chance to evaluate resistance in virologically suppressed HIV infected patients. OBJECTIVES To evaluate the impact of baseline resistance detected through PBMC GRT on virological rebound after switching treatment. STUDY DESIGN Baseline genotypic susceptibility scores (GSS) from PBMC GRT (DNA-GSS) and from previous cumulative plasma GRTs (when available, pRNA-GSS) were evaluated. Survival analysis was used to assess the probability and predictors of virological rebound (VR). RESULTS 227 virologically suppressed patients were analysed. Twenty-four months after switching therapy, the probability of VR was 15.3%. Patients showing an intermediate or full resistant DNA-GSS had a higher probability of experiencing VR compared to those carrying a fully susceptible DNA-GSS (27.2% vs. 13.7%, p = 0.001). By multivariable Cox regression, patients with an intermediate/full resistant DNA-GSS, with a nadir CD4 count <100 cell/mm3 and with a shorter time of previous virological suppression showed a higher adjusted hazard of experiencing VR. In a sub-group of 114 patients with previous plasma GRTs available, patients with an intermediate or fully resistance showed by both GSSs (from plasma and PBMCs) had the highest probability of experiencing VR. CONCLUSIONS Resistance detected in proviral DNA, together with a low nadir CD4 count and a short previous virological control, predicts VR after therapy switching in virologically suppressed patients. PBMC GRT can be a useful tool for tailoring treatment switch, especially if paired with information about previous cumulative resistance and previous viro-immunological history.
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Affiliation(s)
| | - Mauro Zaccarelli
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy.
| | | | | | | | - Alberto Giannetti
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Federica Forbici
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Ada Bertoli
- University of Rome "Tor Vergata", Rome, Italy
| | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Carmela Pinnetti
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | | | | | | | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
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15
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Lack of impact of pre-existing T97A HIV-1 integrase mutation on integrase strand transfer inhibitor resistance and treatment outcome. PLoS One 2017; 12:e0172206. [PMID: 28212411 PMCID: PMC5315389 DOI: 10.1371/journal.pone.0172206] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/23/2017] [Indexed: 01/05/2023] Open
Abstract
T97A is an HIV-1 integrase polymorphism associated with integrase strand transfer inhibitor (INSTI) resistance. Using pooled data from 16 clinical studies, we investigated the prevalence of T97A (pre-existing and emergent) and its impact on INSTI susceptibility and treatment response in INSTI-naive patients who enrolled on elvitegravir (EVG)- or raltegravir (RAL)-based regimens. Prior to INSTI-based therapy, primary INSTI resistance-associated mutations (RAMs) were absent and T97A pre-existed infrequently (1.4%; 47 of 3367 integrase sequences); most often among non-B (5.3%) than B (0.9%) HIV-1 subtypes. During INSTI-based therapy, few patients experienced virologic failure with emergent INSTI RAMs (3%; 122 of 3881 patients), among whom T97A emerged infrequently in the presence (n = 6) or absence (n = 8) of primary INSTI RAMs. A comparison between pre-existing and emergent T97A patient populations (i.e., in the absence of primary INSTI RAMs) showed no significant differences in EVG or RAL susceptibility in vitro. Furthermore, among all T97A-containing viruses tested, only 38-44% exhibited reduced susceptibility to EVG and/or RAL (all of low magnitude; <11-fold), while all maintained susceptibility to dolutegravir. Of the patients with pre-existing T97A, 17 had available clinical follow-up: 16 achieved virologic suppression and 1 maintained T97A and INSTI sensitivity without further resistance development. Overall, T97A is an infrequent integrase polymorphism that is enriched among non-B HIV-1 subtypes and can confer low-level reduced susceptibility to EVG and/or RAL. However, detection of T97A does not affect response to INSTI-based therapy with EVG or RAL. These results suggest a very low risk of initiating INSTI-based therapy in patients with pre-existing T97A.
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16
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Zaccarelli M, Santoro MM, Armenia D, Borghi V, Gennari W, Gori C, Forbici F, Bertoli A, Fabeni L, Giannetti A, Cicalini S, Bellagamba R, Andreoni M, Mastroianni CM, Mussini C, Ceccherini-Silberstein F, Perno CF, Antinori A. Genotypic resistance test in proviral DNA can identify resistance mutations never detected in historical genotypic test in patients with low level or undetectable HIV-RNA. J Clin Virol 2016; 82:94-100. [PMID: 27472519 DOI: 10.1016/j.jcv.2016.07.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/17/2016] [Accepted: 07/15/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Beyond the detection of resistant HIV strains found in plasma samples, archival HIV-DNA in peripheral blood mononuclear cells (PBMCs) might represent a reservoir of additional resistance. OBJECTIVE To characterize the HIV-1 resistance in PBMCs from patients with suppressed or low-level viremia (50-1000 copies/mL) and evaluate its added value compared to the resistance detected in previous plasma genotypic resistance tests (GRTs). STUDY DESIGN HIV-1 infected patients selected for treatment change despite low/undetectable viremia were tested. Number and type of primary resistance mutations (PRMs) detected in PBMCs were compared to those detected in previous plasma GRTs. Logistic regression assessed factors associated with presence of at least one PRM in PBMCs. RESULT 468 patients with a PBMC GRT were analyzed; 149 of them had at least 2 plasma GRTs performed before PBMC genotyping. 42.3% of patients showed at least one PRM in PBMCs. The highest proportion of PRMs in PBMCs was observed for NRTI class (30.6%), followed by NNRTI (22.2%), PI (14.1%) and INI (4.9%). In 20.1% of patients, PRMs were detected only in PBMCs and not in any of the plasma GRT previously performed. By using multivariable analysis, a higher number of previous regimens, injecting drug-use route and a lower nadir CD4 were associated with significantly higher risk of detecting PRMs in PBMCs. CONCLUSION Our findings support the usage of PBMC GRT in addition to the current recommended plasma RNA test, especially when therapeutic and/or resistance information is not available.
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Affiliation(s)
- Mauro Zaccarelli
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | | | | | | | - Caterina Gori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Federica Forbici
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | - Lavinia Fabeni
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Alberto Giannetti
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Stefania Cicalini
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | - Rita Bellagamba
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
| | | | | | | | | | | | - Andrea Antinori
- National Institute for Infectious Diseases L. Spallanzani, IRCCS, Rome, Italy
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Brenner BG, Wainberg MA. Clinical benefit of dolutegravir in HIV-1 management related to the high genetic barrier to drug resistance. Virus Res 2016; 239:1-9. [PMID: 27422477 DOI: 10.1016/j.virusres.2016.07.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/07/2016] [Accepted: 07/11/2016] [Indexed: 01/08/2023]
Abstract
This manuscript reviews the reasons why Integrase inhibitors should now routinely constitute a part of first line antiretroviral therapy for the treatment of HIV disease. The use of these drugs that are generally well tolerated has resulted in far less drug resistance than was the case with most other categories of antiviral compounds. In addition, the integrase inhibitor family of drugs has been less prone to the problem of transmitted drug resistance which is due to a wide variety of substitutions in the HIV genome that can be sexually transmitted from one person to another. However, the use of integrase inhibitors in first line therapy may unfortunately not soon happen in developing country settings where non-nucleoside reverse transcriptase inhibitors continue to be a mainstay of initial therapy, primarily for reasons of cost. As long as this situation continues, problems of drug resistance and transmitted drug resistance will be common in such settings. Current evidence also suggests that the use of dolutegravir as a first line integrase inhibitor may limit development of drug resistance to an extent that exceeds the use of other members of this family of drugs. This may be due to particular patterns of resistance involving dolutegravir, whereby the mutations that are associated with resistance against this compound may actually diminish both HIV replication capacity as well as integrase enzymatic activity in a far-reaching and unique manner. This gives potential hope that the use of dolutegravir in first line therapy could actually form part of the long-sought goal of attainment of a functional cure for HIV disease.
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Affiliation(s)
- Bluma G Brenner
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.
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18
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Armenia D, Di Carlo D, Maffongelli G, Borghi V, Alteri C, Forbici F, Bertoli A, Gori C, Giuliani M, Nicastri E, Zaccarelli M, Pinnetti C, Cicalini S, D'Offizi G, Ceccherini-Silberstein F, Mussini C, Antinori A, Andreoni M, Perno CF, Santoro MM. Virological response and resistance profile in HIV-1-infected patients starting darunavir-containing regimens. HIV Med 2016; 18:21-32. [PMID: 27353061 DOI: 10.1111/hiv.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVES We evaluated the virological response in patients starting a regimen based on darunavir/ritonavir (DRV/r), which is currently the most widely used ritonavir-boosted protease inhibitor. METHODS Data from 206 drug-naïve and 327 PI-experienced patients starting DRV/r 600/100 mg twice daily (DRV600) or 800/100 mg once daily (DRV800) were examined. The probabilities of virological success (VS) and virological rebound (VR) were evaluated in survival analyses. Baseline DRV/r resistance and its evolution at failure were also examined. RESULTS DRV600 was preferentially administered in patients with complex requirements (older age, higher viraemia, lower CD4 cell count and DRV/PI resistance) compared with DRV800. By 12 months, the probability of achieving VS was 93.2% and 84.3% in drug-naïve and PI-experienced patients, respectively. The higher the baseline viraemia, the longer was the time required to achieve VS, both in drug-naïve patients [>500 000 HIV-1 RNA copies/mL: median [interquartile range (IQR)] 6.1 (5.1-10.3) months; 100 000-500 000 copies/mL: median (IQR) 4.9 (3.8-6.1) months; <100 000 copies/mL: median (IQR) 3.9 (3.5-4.8) months; P < 0.001] and in PI-experienced patients [≥100 000 copies/mL: median (IQR) 7.2 (5.7-11.6) months; <100 000 copies/mL: median (IQR) 2.8 (2.4-3.3) months; P < 0.001]. In PI-experienced patients, the probability of VR was higher for higher viraemia levels (22.3% for ≥100 000 copies/ml vs. 9.7% for <100 000 copies/mL; P = 0.007). Baseline resistance did not affect the virological response. At failure, a high percentage of patients maintained virus susceptible to all PIs (drug-naïve: 95%; PI-experienced: 80%). Despite being used more often in patients with more complex requirements, DRV600 performed as well as DRV800. CONCLUSIONS In clinical practice, use of DRV/r (with its flexible dosage) results in high rates of virological response. These data support the use of PI/r in patients whose characteristics require potent drugs with a high genetic barrier.
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Affiliation(s)
- D Armenia
- Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - D Di Carlo
- Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - G Maffongelli
- Infectious Diseases Division, University Hospital Tor Vergata, Rome, Italy
| | - V Borghi
- Infectious Diseases Division, Modena University Hospital, Modena, Italy
| | - C Alteri
- Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | - F Forbici
- Antiretroviral Therapy Monitoring Unit, L Spallanzani Hospital, Rome, Italy
| | - A Bertoli
- Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.,Molecular Virology Division, University Hospital Tor Vergata, Rome, Italy
| | - C Gori
- Antiretroviral Therapy Monitoring Unit, L Spallanzani Hospital, Rome, Italy
| | - M Giuliani
- Infectious Dermatology Unit, San Gallicano Hospital, Rome, Italy
| | - E Nicastri
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | - M Zaccarelli
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | - C Pinnetti
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | - S Cicalini
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | - G D'Offizi
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | | | - C Mussini
- Infectious Diseases Division, Modena University Hospital, Modena, Italy
| | - A Antinori
- Infectious Diseases Division, L Spallanzani Hospital, Rome, Italy
| | - M Andreoni
- Infectious Diseases Division, University Hospital Tor Vergata, Rome, Italy
| | - C F Perno
- Antiretroviral Therapy Monitoring Unit, L Spallanzani Hospital, Rome, Italy
| | - M M Santoro
- Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
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Abstract
Dolutegravir (DTG) is a second-generation integrase strand transfer inhibitor (INSTI), which has now been licensed to be used in different countries including the UK. Earlier studies have demonstrated that DTG when used with nucleoside backbone in treatment-naïve and - experienced patients has been well tolerated and demonstrated virological suppression comparable to other INSTIs and superiority against other first-line agents, including efavirenz and boosted protease inhibitors. Like other INSTIs, DTG uses separate metabolic pathways compared to other antiretrovirals and is a minor substrate for CYP-450. It does not appear to have a significant interaction with drugs, which uses the CYP-450 system. Nonetheless, it uses renal solute transporters that may potentially inhibit the transport of other drugs and can have an effect on the elimination of other drugs. However, the impact of this mechanism appears to be very minimal and insignificant clinically. The side effect profiles of DTG are similar to raltegravir and have been found to be well tolerated. DTG has a long plasma half-life and is suitable for once daily use without the need for a boosting agent. DTG has all the potential to be used as a first-line drug in combination with other nucleoside backbones, especially in the form of a single tablet in combination with abacavir and lamivudine. The purpose of this review article is to present the summary of the available key information about the clinical usefulness of DTG in the treatment of HIV infection.
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Affiliation(s)
- Huda Taha
- Integrated Sexual Health Service Coventry and Warwickshire Partnership NHS Trust, Coventry, UK
| | - Archik Das
- School of Medicine, Birmingham University, Birmingham, UK
| | - Satyajit Das
- Integrated Sexual Health Service Coventry and Warwickshire Partnership NHS Trust, Coventry, UK ; Coventry University, Coventry, UK
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Vancoillie L, Mortier V, Demecheleer E, Schauvliege M, Vandekerckhove L, Vogelaers D, Verhofstede C. Drug resistance is rarely the cause or consequence of long-term persistent low-level viraemia in HIV-1-infected patients on ART. Antivir Ther 2015; 20:789-94. [PMID: 25945956 DOI: 10.3851/imp2966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND The introduction of highly sensitive HIV-1 viral load assays with a lower quantification limit of 20 copies/ml uncovered that in a number of patients on ART, the viral load systematically fluctuates around or slightly above the detection limit of the assays. This study aimed to analyse the presence or occurrence of drug resistance mutations in HIV-1-infected patients during long-term persistent low-level viraemia (PLLV) under ART. METHODS A retrospective study was carried out in which baseline and on-therapy presence of drug resistance mutations in the HIV-1 protease and reverse transcriptase genes were analysed in patients with PLLV between 20 and 250 copies/ml. For all available plasma samples collected during PLLV, resistance analysis was attempted with an ultrasensitive amplification and sequencing protocol. RESULTS Resistance analysis was successful for 154 samples collected longitudinally from 23 patients over a median period of 4.7 years (IQR 3.3-5.7). Twenty of these patients were on a boosted protease inhibitor (PI)-based regimen (87%). Single drug resistance mutations were detected in isolated samples of 4 patients, 2 of the 3 patients who initiated a non-nucleoside reverse transcriptase inhibitor-based regimen and 2 of the 20 on a PI-based regimen. Only one of the detected mutations decreased susceptibility to the therapy regimen taken at the time of sample collection. Drug resistance mutations were not found in the three patients who developed virological failure (viral load >250 copies/ml) during the study. CONCLUSIONS Long episodes of PLLV in patients on boosted PI-based regimens rarely result in the selection of new drug-resistant variants.
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Affiliation(s)
- Leen Vancoillie
- AIDS Reference Laboratory, Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, Ghent, Belgium
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