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Maruapula D, MacLeod IJ, Moyo S, Musonda R, Seatla K, Molebatsi K, Leteane M, Essex M, Gaseitsiwe S, Rowley CF. Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana. AAS Open Res 2021; 3:50. [PMID: 34036243 PMCID: PMC8112461 DOI: 10.12688/aasopenres.13107.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs). Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants. There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.
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Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Iain J. MacLeod
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Aldatu Biosciences, Watertown, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - Kaelo Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | | | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Christopher F. Rowley
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Beth Israel Deaconess Medical Center, Boston, MA, USA
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Maruapula D, MacLeod IJ, Moyo S, Musonda R, Seatla K, Molebatsi K, Leteane M, Essex M, Gaseitsiwe S, Rowley CF. Use of a mutation-specific genotyping method to assess for HIV-1 drug resistance in antiretroviral-naïve HIV-1 Subtype C-infected patients in Botswana. AAS Open Res 2020; 3:50. [PMID: 34036243 PMCID: PMC8112461 DOI: 10.12688/aasopenres.13107.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2020] [Indexed: 10/20/2023] Open
Abstract
Background: HIV-1 drug resistance poses a major threat to the success of antiretroviral therapy. The high costs of available HIV drug resistance assays prohibit their routine usage in resource-limited settings. Pan-degenerate amplification and adaptation (PANDAA), a focused genotyping approach based on quantitative PCR (qPCR), promises a fast and cost-effective way to detect HIV drug resistance mutations (HIVDRMs). Given the high cost of current genotyping methods, we sought to use PANDAA for screening key HIVDRMs in antiretroviral-naïve individuals at codons 103, 106 and 184 of the HIV-1 reverse transcriptase gene. Mutations selected at these positions have been shown to be the most common driver mutations in treatment failure. Methods: A total of 103 samples from antiretroviral-naïve individuals previously genotyped by Sanger population sequencing were used to assess and verify the performance of PANDAA. PANDAA samples were run on the ABI 7500 Sequence Detection System to genotype the K103N, V106M and M184V HIVDRMs. In addition, the cost per sample and reaction times were compared. Results: Sanger population sequencing and PANDAA detected K103N mutation in three (2.9%) out of 103 participants. There was no evidence of baseline V106M and M184V mutations observed in our study. To genotype the six HIVDRMs it costs approximately 40 USD using PANDAA, while the reagents cost per test for Sanger population sequencing is approximately 100 USD per sample. PANDAA was performed quicker compared to Sanger sequencing, 2 hours for PANDAA versus 15 hours for Sanger sequencing. Conclusion: The performance of PANDAA and Sanger population sequencing demonstrated complete concordance. PANDAA could improve patient management by providing quick and relatively cheap access to drug-resistance information.
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Affiliation(s)
- Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Iain J. MacLeod
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Aldatu Biosciences, Watertown, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | | | - Kaelo Seatla
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | - Kesaobaka Molebatsi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- University of Botswana, Gaborone, Botswana
| | | | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H Chan School of Public Health, Boston, MA, USA
| | - Christopher F. Rowley
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Beth Israel Deaconess Medical Center, Boston, MA, USA
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Gudipati S, Brar I, Golembieski A, Hanna Z, Markowitz N. Occurrence of the S230R integrase strand inhibitor mutation in a treatment-naïve individual case report. Medicine (Baltimore) 2020; 99:e20915. [PMID: 32629687 PMCID: PMC7337458 DOI: 10.1097/md.0000000000020915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Transmitted resistance to integrase strand inhibitors (INSTI) has been uncommon, but is slowly becoming more prevalent among those living with HIV. In an era with 2-drug regimens for antiretroviral therapy, transmitted resistance for INSTI is alarming. PATIENT CONCERNS A 28-year-old African American female was recently diagnosed with HIV during a 30-week prenatal visit. DIAGNOSIS HIV 4th generation test was positive as well as confirmation. Genotype was performed using next generation sequencing. INTERVENTIONS Patient was initially rapidly started on a dolutegravir based regimen and changed to a protease inhibitor regimen once her genotype reported an S230R mutation. OUTCOMES Patient became virally suppressed on antiretroviral therapy and delivered an HIV negative baby. LESSONS INSTI resistance testing should be done for treatment-naïve and INSTI-naïve persons, particularly when considering 2 drug INSTI based regimens.
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Panpradist N, Beck IA, Vrana J, Higa N, McIntyre D, Ruth PS, So I, Kline EC, Kanthula R, Wong-On-Wing A, Lim J, Ko D, Milne R, Rossouw T, Feucht UD, Chung M, Jourdain G, Ngo-Giang-Huong N, Laomanit L, Soria J, Lai J, Klavins ED, Frenkel LM, Lutz BR. OLA-Simple: A software-guided HIV-1 drug resistance test for low-resource laboratories. EBioMedicine 2019; 50:34-44. [PMID: 31767540 PMCID: PMC6921160 DOI: 10.1016/j.ebiom.2019.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/21/2023] Open
Abstract
Background HIV drug resistance (HIVDR) testing can assist clinicians in selecting treatments. However, high complexity and cost of genotyping assays limit routine testing in settings where HIVDR prevalence has reached high levels. Methods The oligonucleotide ligation assay (OLA)-Simple kit was developed for detection of HIVDR against first-line non-nucleoside/nucleoside reverse transcriptase inhibitors and validated on 672 codons (168 specimens) from subtypes A, B, C, D, and AE. The kit uses dry reagents to facilitate assay setup, lateral flow devices for visual HIVDR detections, and in-house software with an interface for guiding users and analyzing results. Findings HIVDR analysis of specimens by OLA-Simple compared to Sanger sequencing revealed 99.6 ± 0.3% specificity and 98.2 ± 0.9% sensitivity, and compared to high-sensitivity assays, 99.6 ± 0.6% specificity and 86.2 ± 2.5% sensitivity, with 2.6 ± 0.9% indeterminate results. OLA-Simple was performed more rapidly compared to Sanger sequencing (<4 h vs. 35–72 h). Forty-one untrained volunteers blindly tested two specimens each with 96.8 ± 0.8% accuracy. Interpretation OLA-Simple compares favorably with HIVDR genotyping by Sanger and sensitive comparators. Instructional software enabled inexperienced, first-time users to perform the assay with high accuracy. The reduced complexity, cost, and training requirements of OLA-Simple could improve access to HIVDR testing in low-resource settings and potentially allow same-day selection of appropriate antiretroviral therapy. Fund USA National Institutes of Health R01; the Clinical and Retrovirology Research Core and the Molecular Profiling and Computational Biology Core of the UW CFAR; Seattle Children's Research Institute; UW Holloman Innovation Challenge Award; Pilcher Faculty Fellowship.
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Affiliation(s)
- Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Global WACh Program, Department of Global Health, University of Washington, Seattle, WA 98104, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Justin Vrana
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Nikki Higa
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - David McIntyre
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Parker S Ruth
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Isaac So
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Enos C Kline
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ruth Kanthula
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Medstar Georgetown University Hospital, DC, 20007, USA
| | - Annie Wong-On-Wing
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Jonathan Lim
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Daisy Ko
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Ross Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Theresa Rossouw
- Department of Immunology, University of Pretoria, Pretoria 0002, South Africa
| | - Ute D Feucht
- Research Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, Department of Paediatrics, University of Pretoria, Pretoria 0002, South Africa; Research Unit for Maternal and Infant Health Care Strategies, South African Medical Research Council, Kalafong Hospital, Atteridgeville 0008, South Africa
| | - Michael Chung
- Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Epidemiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Medicine, Aga Khan University, Nairobi, Kenya
| | - Gonzague Jourdain
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Nicole Ngo-Giang-Huong
- Institut de Recherche pour le Développement IRD U174 PHPT, Chiang Mai 50000, Thailand; Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Laddawan Laomanit
- Faculty of Associated Medical Sciences, Division of Clinical Microbiology, Chiang Mai 50200, Thailand
| | - Jaime Soria
- Department of Infectious Diseases, Hospital Nacional Dos de Mayo, Av. Miguel Grau 13, Cercado de Lima 15003, Peru
| | - James Lai
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Eric D Klavins
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA; Departments of Electrical Engineering and Paul G. Allen Center for Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Lisa M Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Division of Infectious Diseases, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Division of Virology, Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
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Major drug resistance mutations to HIV-1 protease inhibitors (PI) among patients exposed to PI class failing antiretroviral therapy in São Paulo State, Brazil. PLoS One 2019; 14:e0223210. [PMID: 31574109 PMCID: PMC6772045 DOI: 10.1371/journal.pone.0223210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/15/2019] [Indexed: 11/21/2022] Open
Abstract
Background Protease inhibitors (PI) are especially important in salvage therapy. Previous treatment failure with a PI containing regimen may elicit resistance mutations, reducing PI susceptibility and limiting treatment options. The aim of this study was to describe major PI mutations among patients exposed to at least one PI to evaluate predictors of mutation emergence and the impact of subtypes on resistance. Methodology Partial HIV-1 pol sequences (Sanger Sequencing) from patients exposed to PI with virological failure were genotyped from January 2014 to December 2017. Drug resistance mutations (DRM), antiretroviral susceptibility (GSS) and subtypes, along clinical and laboratory parameters, were evaluated using logistic regression to access the predictors of mutation emergence. Results In 27.5% (466/1696) of the cases at least one major PI mutations was identified, most commonly M46 (14.7%), V82 (13.8%) and I54 (13.3%). Mutations to NRTI and NNRTI were observed in 69.6% and 59.9%, respectively, of the 1696 sequences. Full activity to darunavir was predicted in 88% (1496/1696), but was only 57% among those with at least one PI-DRM. Subtype C sequences had less major PI-DRMs (10%, 9/87) compared to B (28%, 338/1216) or F (35%, 58/168) (p <0.001) but adjusted analysis suggested that this association is not independent from a shorter treatment time and fewer regimens (OR 0.59, Confidence Interval 95: 0.2–2.5, p = 0.48). Subtype F, together with NRTI mutations and longer time on treatment was associated to presence of PI-DRM, to a lower darunavir GSS and to mutations at codon I50. Conclusions Among patients with PI-DRM, full activity to darunavir was compromised in almost half of the cases and efforts to detect failure at earlier time are warranted, particularly for HIV-1 subtype F that showed association to the emergence of resistance, with potential impact in protease inhibitors sequencing. Furthermore, NRTI mutations may serve as an indicative of sufficient adherence to allow PI-DRM emergence.
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Rusere LN, Lockbaum GJ, Lee SK, Henes M, Kosovrasti K, Spielvogel E, Nalivaika EA, Swanstrom R, Yilmaz NK, Schiffer CA, Ali A. HIV-1 Protease Inhibitors Incorporating Stereochemically Defined P2' Ligands To Optimize Hydrogen Bonding in the Substrate Envelope. J Med Chem 2019; 62:8062-8079. [PMID: 31386368 DOI: 10.1021/acs.jmedchem.9b00838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A structure-guided design strategy was used to improve the resistance profile of HIV-1 protease inhibitors by optimizing hydrogen bonding and van der Waals interactions with the protease while staying within the substrate envelope. Stereoisomers of 4-(1-hydroxyethyl)benzene and 4-(1,2-dihydroxyethyl)benzene moieties were explored as P2' ligands providing pairs of diastereoisomers epimeric at P2', which exhibited distinct potency profiles depending on the configuration of the hydroxyl group and size of the P1' group. While compounds with the 4-(1-hydroxyethyl)benzene P2' moiety maintained excellent antiviral potency against a panel of multidrug-resistant HIV-1 strains, analogues with the polar 4-(1,2-dihydroxyethyl)benzene moiety were less potent, and only the (R)-epimer incorporating a larger 2-ethylbutyl P1' group showed improved potency. Crystal structures of protease-inhibitor complexes revealed strong hydrogen bonding interactions of both (R)- and (S)-stereoisomers of the hydroxyethyl group with Asp30'. Notably, the (R)-dihydroxyethyl group was involved in a unique pattern of direct hydrogen bonding interactions with the backbone amides of Asp29' and Asp30'. The SAR data and analysis of crystal structures provide insights for optimizing these promising HIV-1 protease inhibitors.
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Affiliation(s)
- Linah N Rusere
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Gordon J Lockbaum
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Mina Henes
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Klajdi Kosovrasti
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Ean Spielvogel
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina 27599 , United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology , University of Massachusetts Medical School , Worcester , Massachusetts 01605 , United States
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Halogen Bond Interactions of Novel HIV-1 Protease Inhibitors (PI) (GRL-001-15 and GRL-003-15) with the Flap of Protease Are Critical for Their Potent Activity against Wild-Type HIV-1 and Multi-PI-Resistant Variants. Antimicrob Agents Chemother 2019; 63:AAC.02635-18. [PMID: 30962341 DOI: 10.1128/aac.02635-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/03/2019] [Indexed: 01/29/2023] Open
Abstract
We generated two novel nonpeptidic HIV-1 protease inhibitors (PIs), GRL-001-15 and GRL-003-15, which contain unique crown-like tetrahydropyranofuran (Crn-THF) and P2'-cyclopropyl-aminobenzothiazole (Cp-Abt) moieties as P2 and P2' ligands, respectively. GRL-001-15 and GRL-003-15 have meta-monofluorophenyl and para-monofluorophenyl at the P1 site, respectively, exert highly potent activity against wild-type HIV-1 with 50% effective concentrations (EC50s) of 57 and 50 pM, respectively, and have favorable cytotoxicity profiles with 50% cytotoxic concentrations (CC50s) of 38 and 11 μM, respectively. The activity of GRL-001-15 against multi-PI-resistant HIV-1 variants was generally greater than that of GRL-003-15. The EC50 of GRL-001-15 against an HIV-1 variant that was highly resistant to multiple PIs, including darunavir (DRV) (HIV-1DRV R P30), was 0.17 nM, and that of GRL-003-15 was 3.3 nM, while DRV was much less active, with an EC50 of 216 nM. The emergence of HIV-1 variants resistant to GRL-001-15 and GRL-003-15 was significantly delayed compared to that of variants resistant to selected PIs, including DRV. Structural analyses of wild-type protease (PRWT) complexed with the novel PIs revealed that GRL-001-15's meta-fluorine atom forms halogen bond interactions (2.9 and 3.0 Å) with Gly49 and Ile50, respectively, of the protease flap region and with Pro81' (2.7 and 3.2 Å), which is located close to the protease active site, and that two fluorine atoms of GRL-142-13 form multiple halogen bond interactions with Gly49, Ile50, Pro81', Ile82', and Arg8'. In contrast, GRL-003-15 forms halogen bond interactions with Pro81' alone, suggesting that the reduced antiviral activity of GRL-003-15 is due to the loss of the interactions with the flap region.
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Sili U, Aksu B, Tekin A, Hasdemir U, Soyletir G, Korten V. Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra- Deep Pyrosequencing in a Turkish Cohort. Curr HIV Res 2019; 16:216-221. [PMID: 30198436 DOI: 10.2174/1570162x16666180910130112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antiretroviral treatment (ART) reduces morbidity and mortality caused by human immunodeficiency virus (HIV) infection; however, the emergence of drug-resistant strains poses an important obstacle to treatment success. Using conventional sequencing methods to determine antiretroviral resistance, mutations present in ≥20% of quasispecies can be identified, but drug-resistant minority variants can lead to virologic failure. OBJECTIVE We aimed to assess transmitted drug resistance mutations (TDRMs) within minority variants using ultra-deep pyrosequencing (UDPS). METHOD Treatment-naive adult patients were included in this observational study. Surveillance TDRMs were classified as ≥20% or at minority variant level (≥2% - <20%). Genotypic sensitivity score calculated by using all pre-treatment drug resistance mutations (PDRMs) was also evaluated. RESULTS Thirty-six patients were analyzed. Any TDRM at ≥20% level was detected in 8.3% of the patients (n=3). This prevalence increased to 30.6% (n=11) with the inclusion of minority variants. All non-nucleoside reverse transcriptase inhibitor and protease inhibitor-related TDRMs were within minority variants. The genotypic sensitivity score of rilpivirine-based regimens was considerably diminished when minority variants were included in the PDRM analysis. CONCLUSION UDPS was used for the first time to assess TDRM in a Turkish HIV cohort and uncovered several mutations hidden within minority variants. UDPS may be preferred to detect PDRMs for avoiding virologic failure with rilpivirine-based ART regimens.
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Affiliation(s)
- Uluhan Sili
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Burak Aksu
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Aysun Tekin
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Ufuk Hasdemir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Guner Soyletir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Volkan Korten
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
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Mutations in the HIV-1 envelope glycoprotein can broadly rescue blocks at multiple steps in the virus replication cycle. Proc Natl Acad Sci U S A 2019; 116:9040-9049. [PMID: 30975760 DOI: 10.1073/pnas.1820333116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The p6 domain of HIV-1 Gag contains highly conserved peptide motifs that recruit host machinery to sites of virus assembly, thereby promoting particle release from the infected cell. We previously reported that mutations in the YPXnL motif of p6, which binds the host protein Alix, severely impair HIV-1 replication. Propagation of the p6-Alix binding site mutants in the Jurkat T cell line led to the emergence of viral revertants containing compensatory mutations not in Gag but in Vpu and the envelope (Env) glycoprotein subunits gp120 and gp41. The Env compensatory mutants replicate in Jurkat T cells and primary human peripheral blood mononuclear cells, despite exhibiting severe defects in cell-free particle infectivity and Env-mediated fusogenicity. Remarkably, the Env compensatory mutants can also rescue a replication-delayed integrase (IN) mutant, and exhibit reduced sensitivity to the IN inhibitor Dolutegravir (DTG), demonstrating that they confer a global replication advantage. In addition, confirming the ability of Env mutants to confer escape from DTG, we performed de novo selection for DTG resistance and observed resistance mutations in Env. These results identify amino acid substitutions in Env that confer broad escape from defects in virus replication imposed by either mutations in the HIV-1 genome or by an antiretroviral inhibitor. We attribute this phenotype to the ability of the Env mutants to mediate highly efficient cell-to-cell transmission, resulting in an increase in the multiplicity of infection. These findings have broad implications for our understanding of Env function and the evolution of HIV-1 drug resistance.
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Van Rompay KKA, Hassounah S, Keele BF, Lifson JD, Ardeshir A, Watanabe J, Pham HT, Chertova E, Sowder R, Balzarini J, Mesplède T, Wainberg MA. Dolutegravir Monotherapy of Simian Immunodeficiency Virus-Infected Macaques Selects for Several Patterns of Resistance Mutations with Variable Virological Outcomes. J Virol 2019; 93:e01189-18. [PMID: 30381490 PMCID: PMC6321921 DOI: 10.1128/jvi.01189-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 10/24/2018] [Indexed: 12/19/2022] Open
Abstract
Drug resistance remains a major concern for human immunodeficiency virus (HIV) treatment. To date, very few resistance mutations have emerged in first-line combination therapy that includes the integrase strand transfer inhibitor (INSTI) dolutegravir (DTG). In vitro, DTG selects for several primary mutations that induce low-level DTG resistance; secondary mutations, while increasing the level of resistance, however, further impair replication fitness, which raised the idea that DTG monotherapy may be feasible. The simian immunodeficiency virus (SIV) rhesus macaque model of HIV infection can be useful to explore this concept. Nine macaques were infected with virulent SIVmac251 and started on DTG monotherapy during either acute (n = 2) or chronic infection (n = 7). Within 4 weeks of treatment, all animals demonstrated a reduction in viremia of 0.8 to 3.5 log RNA copies/ml plasma. Continued treatment led to overall sustained benefits, but the outcome after 10 to 50 weeks of treatment was highly variable and ranged from viral rebound to near pretreatment levels to sustained suppression, with viremia being 0.5 to 5 logs lower than expected based on pretreatment viremia. A variety of mutations previously described to confer low-level resistance of HIV-1 to DTG or other INSTI were detected, and these were sometimes followed by mutations believed to be compensatory. Some mutations, such as G118R, previously shown to severely impair the replication capacity in vitro, were associated with more sustained virological and immunological benefits of continued DTG therapy, while other mutations, such as E92Q and G140A/Q148K, were associated with more variable outcomes. The observed variability of the outcomes in macaques warrants avoidance of DTG monotherapy in HIV-infected people.IMPORTANCE A growing number of anti-HIV drug combinations are effective in suppressing virus replication in HIV-infected persons. However, to reduce their cost and risk for toxicity, there is considerable interest in simplifying drug regimens. A major concern with single-drug regimens is the emergence of drug-resistant viral mutants. It has been speculated that DTG monotherapy may be a feasible option, because DTG may have a higher genetic barrier for the development of drug resistance than other commonly used antiretrovirals. To explore treatment initiation with DTG monotherapy, we started SIV-infected macaques on DTG during either acute or chronic infection. Although DTG initially reduced virus replication, continued treatment led to the emergence of a variety of viral mutations previously described to confer low-level resistance of HIV-1 to DTG, and this was associated with variable clinical outcomes. This unpredictability of mutational pathways and outcomes warns against using DTG monotherapy as initial treatment for HIV-infected people.
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Affiliation(s)
- Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, California, USA
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Said Hassounah
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Jennifer Watanabe
- California National Primate Research Center, University of California, Davis, Davis, California, USA
| | - Hanh Thi Pham
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Elena Chertova
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Raymond Sowder
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Thibault Mesplède
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Mark A Wainberg
- McGill University AIDS Centre Lady Davis Institute for Medical Research, Montreal, Quebec, Canada
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Dessilly G, Goeminne L, Vandenbroucke AT, Dufrasne FE, Martin A, Kabamba-Mukabi B. First evaluation of the Next-Generation Sequencing platform for the detection of HIV-1 drug resistance mutations in Belgium. PLoS One 2018; 13:e0209561. [PMID: 30596682 PMCID: PMC6312258 DOI: 10.1371/journal.pone.0209561] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/12/2018] [Indexed: 12/31/2022] Open
Abstract
Introduction The WHO urges action against the threat posed by HIV drug resistance. It is well known that the sensitivity of Next-Generation Sequencing (NGS) is greater than that of Sanger Sequencing (SS). The objective of this study was to evaluate the performance of the novel NGS HIV-1 drug resistance monitoring system. Materials & methods NGS analyses were performed on 67 plasma samples from HIV-1 infected patients using the Sentosa SQ HIV Genotyping Assay from Vela-Dx. This kit was used on a semi-automated Ion Torrent-based platform. Sequences were compared to those obtained by SS. Samples were analysed in the same and in separate runs. Quality controls (QC) were added to control sequencing processes of protease (PRO), reverse transcriptase (RT) and integrase (INT) regions. Results Of the 41 analysed samples, 33 (80.5%) had identical drug resistance interpretation reports. Discrepant results were observed for eight samples. Five of them were only detected by NGS and had drug resistance mutations (DRMs) with an allelic frequency below the limit of detection of the SS method (between 6.3 to 20.5%). Two DRMs were only identified using the SS method. The sequences were similar in 98.2% of cases (counting variants as mismatches) and homologous in 99.9% if missed variants. Duplicated samples in a single run were similar in 95.7% (99.9%) of cases. Duplicated samples in two different runs were 98% (100%) homologous. QC results were manually assessed with a score of 340/340 for detection of DRMs in PRO and RT and 100% for INT sequencing. Conclusions This is the first preliminary evaluation in Belgium employing the Sentosa SQ HIV Genotyping Assay. The NGS appears to be a promising tool for the detection of DRMs in HIV-1 patients and showed a higher sensitivity compared to SS. Large studies assessing the clinical relevance of low frequency DRMs are needed.
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Affiliation(s)
- Géraldine Dessilly
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
- * E-mail:
| | - Léonie Goeminne
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
| | - Anne-thérèse Vandenbroucke
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
| | - Francois E. Dufrasne
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
| | - Anandi Martin
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
| | - Benoît Kabamba-Mukabi
- Université catholique de Louvain (UCLouvain), Institut de Recherche Expérimentale et Clinique (IREC), Medical Microbiology Unit (MBLG), AIDS Reference Laboratory, Brussels, Belgium
- Université catholique de Louvain (UCLouvain), Cliniques Universitaires Saint-Luc, Clinical Laboratory Department, Brussels, Belgium
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12
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Fulcher JA, Du Y, Zhang TH, Sun R, Landovitz RJ. Emergence of Integrase Resistance Mutations During Initial Therapy Containing Dolutegravir. Clin Infect Dis 2018; 67:791-794. [PMID: 29933437 PMCID: PMC6093998 DOI: 10.1093/cid/ciy228] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/20/2018] [Indexed: 01/09/2023] Open
Abstract
Dolutegravir (DTG) is a preferred drug for initial treatment of human immunodeficiency virus type 1 infection. We present next-generation sequencing analysis of integrase genotypes during a period of virologic failure in a treatment-naive man who initiated tenofovir disoproxil fumarate/emtricitabine plus DTG.
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Affiliation(s)
- Jennifer A Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA)
- VA Greater Los Angeles Healthcare System
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Tian-hao Zhang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA
| | - Raphael J Landovitz
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles (UCLA)
- Center for AIDS Research and Education, Los Angeles, California
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13
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de Miguel R, Montejano R, Stella-Ascariz N, Arribas JR. A safety evaluation of raltegravir for the treatment of HIV. Expert Opin Drug Saf 2017; 17:217-223. [PMID: 29199485 DOI: 10.1080/14740338.2018.1411903] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
INTRODUCTION Raltegravir (RAL) was the first commercialized agent from a new drug class with an innovative target, the integrase. Since its introduction in clinical practice RAL has become widely used for the treatment of HIV-1 infected patients. A decade after its approval, this article reviews key evidence from RAL with a special interest on safety outcomes. Areas covered: Pharmacologic, safety and efficacy data of RAL from clinical trials and post-commercialization published reports are hereby summarized after a literature review including PubMed search, relating proceedings and abstracts from relevant international HIV conferences, assessment reports from European and United States regulatory agencies and treatment guidelines (World Health Organization, United States Department of Health and Human Services and European AIDS Clinical Society), up to October 2017. Most frequent search terms were 'raltegravir', 'safety', 'adverse events', 'efficacy' and 'integrase-inhibitors'. Expert opinion: Despite the arrival of new integrase strand transfer inhibitors (INSTIs) with advantages in terms of dosing convenience (elvitegravir, ELV) and higher genetic barrier (dolutegravir, DTG), RAL has stood the test of time and its overall favourable safety profile, without significant appearance of unexpected adverse events, vouch for its relevance in the antiretroviral armamentarium.
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Affiliation(s)
- Rosa de Miguel
- a HIV Unit, Internal Medicine Service , Hospital Universitario La Paz-IdiPAZ , Madrid , Spain
| | - Rocio Montejano
- a HIV Unit, Internal Medicine Service , Hospital Universitario La Paz-IdiPAZ , Madrid , Spain
| | - Natalia Stella-Ascariz
- a HIV Unit, Internal Medicine Service , Hospital Universitario La Paz-IdiPAZ , Madrid , Spain
| | - Jose R Arribas
- a HIV Unit, Internal Medicine Service , Hospital Universitario La Paz-IdiPAZ , Madrid , Spain
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