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Adawaye C, Fokam J, Kamangu EN, Ngwese DTA, Susin F, Moussa AM, Hig-Zounet B, Mad-Toingué J, Tidjani A, Vaira D, Moutschen M. Performance characteristics of Allele-Specific PCR (ASPCR) in detecting drug resistance mutations among non-B HIV-1 Variants. J Virol Methods 2024; 323:114856. [PMID: 38000668 DOI: 10.1016/j.jviromet.2023.114856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
Allele-Specific Polymerase Chain Reaction (ASPCR) is an affordable point-mutation assay whose validation could improve the detection of HIV-1 drug resistance mutations (DRMs) in resource-limited settings (RLS). We assessed the performance of ASPCR onforty-four non-B HIV-1 plasma samples from patients who were ARV treated in failure in N'Djamena-Chad. Viral RNA was reverse-transcribed and amplified using LightCycler® FastStart DNA MasterPLUS SYBR Green I. Detection of six major DRMs (K70R, K103N, Y181C, M184V, T215F, T215Y) was evaluated on Roche LightCycler®480 automated system (with dilutions 0.01-100%). ASPCR-results were compared to Sanger-sequencing (gold-standard). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). Correlations of mutation curves were excellent (R2 >0.97); all DRMs were detected with desirable mutant/wild-type threshold differences (ΔCt≥9) except K70R(ΔCtK70R=6; ΔCtK103N=13; ΔCtM184V=9; ΔCtT215F=12; ΔCtT215Y=12; ΔCtY181C=9) and positive controls were below required thresholds. Also, ASPCR reproducibility on DRMs was assessed by using dilutions of intra-assay and inter-assay coefficient of variations respectively with a threshold of less than 50(i.e.<0.50 variation) which are;: K70R (0.02-0.28 vs. 0.12-0.37), K103N (0.08-0.42 vs. 0.12-0.37), Y181C (0.12-0.39 vs. 0.31-0.37), M184V (0.13-0.39 vs. 0.23-0.42), T215F (0.05-0.43 vs. 0.04-0.45) and T215Y (0.13-0.41 vs. 0.19-0.41). DRM detection-rate by ASPCR vs Sanger was respectively: M184V (63.6% vs. 38.6%); T215F (18.1% vs. 9.1%); T215Y (6.8% vs. 2.3%); K70R (4.5% vs. 2.3%). K103N (22.7% vs. 13.6%); Y181C (13.6% vs. 11.4%). ASPCR appears more efficient for detecting DRMs on diverse HIV-1 non-B circulating in RLS like Chad.
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Affiliation(s)
- Chatté Adawaye
- National Institute of Sciences and Techniques of Abeche (INSTA), Abeche, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium.
| | - Joseph Fokam
- Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon; Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Buea, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon; National HIV Drug Resistance Surveillance and Prevention Working Group (HIVDRWG), Ministry of Public Health, Yaounde, Cameroon.
| | - Erick Ntambwe Kamangu
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Derrick Tambe Ayuk Ngwese
- Virology Laboratory, Chantal BIYA International Reference Centre for research on HIV/AIDS prevention and management, Yaoundé, Cameroon; Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaounde, Cameroon; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Fabrice Susin
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Ali Mahamat Moussa
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - BertinTchombou Hig-Zounet
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Joseph Mad-Toingué
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Faculty of Human Health Sciences, University of N'Djamena, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Abdelsalam Tidjani
- AIDS Reference Laboratory of Liege, CHU de Liege, Liege, Belgium; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Dolores Vaira
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
| | - Michel Moutschen
- Department of Basic Sciences, Faculty of Medicine, University of Kinshasa, Kinshasa, Democratic Republic of Congo; National Reference General Hospital, N'Djamena, Chad; Infectious Diseases and Internal Medicine Service, University Hospital Center of Liège, Liège, Belgium
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Bou-Antoun S, Rokadiya S, Ashiru-Oredope D, Demirjian A, Sherwood E, Ellaby N, Gerver S, Grossi C, Harman K, Hartman H, Lochen A, Ragonnet-Cronin M, Squire H, Sutton JM, Thelwall S, Tree J, Bahar MW, Stuart DI, Brown CS, Chand M, Hopkins S. COVID-19 therapeutics: stewardship in England and considerations for antimicrobial resistance. J Antimicrob Chemother 2023; 78:ii37-ii42. [PMID: 37995354 PMCID: PMC10666993 DOI: 10.1093/jac/dkad314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
The COVID-19 pandemic saw unprecedented resources and funds driven into research for the development, and subsequent rapid distribution, of vaccines, diagnostics and directly acting antivirals (DAAs). DAAs have undeniably prevented progression and life-threatening conditions in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, there are concerns of antimicrobial resistance (AMR), antiviral resistance specifically, for DAAs. To preserve activity of DAAs for COVID-19 therapy, as well as detect possible mutations conferring resistance, antimicrobial stewardship and surveillance were rapidly implemented in England. This paper expands on the ubiquitous ongoing public health activities carried out in England, including epidemiologic, virologic and genomic surveillance, to support the stewardship of DAAs and assess the deployment, safety, effectiveness and resistance potential of these novel and repurposed therapeutics.
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Affiliation(s)
- Sabine Bou-Antoun
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Sakib Rokadiya
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Diane Ashiru-Oredope
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Alicia Demirjian
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
- Department of Paediatric Infectious Diseases & Immunology, Evelina London Children's Hospital, London, UK
- Faculty of Life Sciences & Medicine, King’s College London, London, UK
| | - Emma Sherwood
- Clinical and Emerging Infections (CEI), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Nicholas Ellaby
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Sarah Gerver
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Carlota Grossi
- COVID-19 Rapid Evidence Service Public Health Advice, Guidance and Expertise (PHAGE), UK Health Security Agency, London NW9 5EQ, UK
| | - Katie Harman
- COVID-19 Vaccines and Applied Epidemiology Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Hassan Hartman
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Alessandra Lochen
- Tuberculosis (TB), Acute Respiratory, Zoonoses, Emerging and Travel infections Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Manon Ragonnet-Cronin
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Hanna Squire
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - J Mark Sutton
- Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
- Institute of Pharmaceutical Sciences, King’s College London, London, UK
| | - Simon Thelwall
- COVID-19 Vaccines and Applied Epidemiology Division, UK Health Security Agency, London NW9 5EQ, UK
| | - Julia Tree
- Research and Evaluation, UK Health Security Agency, Porton Down, Salisbury SP4 0JG, UK
| | - Mohammad W Bahar
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
| | - David I Stuart
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, Oxford, UK
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Colin S Brown
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
| | - Meera Chand
- Genomics Public Health Analysis (GPHA), United Kingdom Health Security Agency (UKHSA), London, UK
| | - Susan Hopkins
- Healthcare-Associated Infection (HCAI), Fungal, Antimicrobial Resistance (AMR), Antimicrobial Use (AMU) & Sepsis Division, United Kingdom Health Security Agency (UKHSA), London, UK
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Insights into HIV-1 Reverse Transcriptase (RT) Inhibition and Drug Resistance from Thirty Years of Structural Studies. Viruses 2022; 14:v14051027. [PMID: 35632767 PMCID: PMC9148108 DOI: 10.3390/v14051027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023] Open
Abstract
The enzyme reverse transcriptase (RT) plays a central role in the life cycle of human immunodeficiency virus (HIV), and RT has been an important drug target. Elucidations of the RT structures trapping and detailing the enzyme at various functional and conformational states by X-ray crystallography have been instrumental for understanding RT activities, inhibition, and drug resistance. The structures have contributed to anti-HIV drug development. Currently, two classes of RT inhibitors are in clinical use. These are nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). However, the error-prone viral replication generates variants that frequently develop resistance to the available drugs, thus warranting a continued effort to seek more effective treatment options. RT also provides multiple additional potential druggable sites. Recently, the use of single-particle cryogenic electron microscopy (cryo-EM) enabled obtaining structures of NNRTI-inhibited HIV-1 RT/dsRNA initiation and RT/dsDNA elongation complexes that were unsuccessful by X-ray crystallography. The cryo-EM platform for the structural study of RT has been established to aid drug design. In this article, we review the roles of structural biology in understanding and targeting HIV RT in the past three decades and the recent structural insights of RT, using cryo-EM.
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Wymant C, Bezemer D, Blanquart F, Ferretti L, Gall A, Hall M, Golubchik T, Bakker M, Ong SH, Zhao L, Bonsall D, de Cesare M, MacIntyre-Cockett G, Abeler-Dörner L, Albert J, Bannert N, Fellay J, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos RD, Laeyendecker O, Meyer L, Porter K, Ristola M, van Sighem A, Berkhout B, Kellam P, Cornelissen M, Reiss P, Fraser C, Aubert V, Battegay M, Bernasconi E, Böni J, Braun DL, Bucher HC, Burton-Jeangros C, Calmy A, Cavassini M, Dollenmaier G, Egger M, Elzi L, Fehr J, Fellay J, Furrer H, Fux CA, Gorgievski M, Günthard H, Haerry D, Hasse B, Hirsch HH, Hoffmann M, Hösli I, Kahlert C, Kaiser L, Keiser O, Klimkait T, Kouyos R, Kovari H, Ledergerber B, Martinetti G, de Tejada BM, Marzolini C, Metzner K, Müller N, Nadal D, Nicca D, Pantaleo G, Rauch A, Regenass S, Rudin C, Schöni-Affolter F, Schmid P, Speck R, Stöckle M, Tarr P, Trkola A, Vernazza P, Weber R, Yerly S, van der Valk M, Geerlings SE, Goorhuis A, Hovius JW, Lempkes B, Nellen FJB, van der Poll T, Prins JM, Reiss P, van Vugt M, Wiersinga WJ, Wit FWMN, van Duinen M, van Eden J, Hazenberg A, van Hes AMH, Rajamanoharan S, Robinson T, Taylor B, Brewer C, Mayr C, Schmidt W, Speidel A, Strohbach F, Arastéh K, Cordes C, Pijnappel FJJ, Stündel M, Claus J, Baumgarten A, Carganico A, Ingiliz P, Dupke S, Freiwald M, Rausch M, Moll A, Schleehauf D, Smalhout SY, Hintsche B, Klausen G, Jessen H, Jessen A, Köppe S, Kreckel P, Schranz D, Fischer K, Schulbin H, Speer M, Weijsenfeld AM, Glaunsinger T, Wicke T, Bieniek B, Hillenbrand H, Schlote F, Lauenroth-Mai E, Schuler C, Schürmann D, Wesselmann H, Brockmeyer N, Jurriaans S, Gehring P, Schmalöer D, Hower M, Spornraft-Ragaller P, Häussinger D, Reuter S, Esser S, Markus R, Kreft B, Berzow D, Back NKT, Christl A, Meyer A, Plettenberg A, Stoehr A, Graefe K, Lorenzen T, Adam A, Schewe K, Weitner L, Fenske S, Zaaijer HL, Hansen S, Stellbrink HJ, Wiemer D, Hertling S, Schmidt R, Arbter P, Claus B, Galle P, Jäger H, Jä Gel-Guedes E, Berkhout B, Postel N, Fröschl M, Spinner C, Bogner J, Salzberger B, Schölmerich J, Audebert F, Marquardt T, Schaffert A, Schnaitmann E, Cornelissen MTE, Trein A, Frietsch B, Müller M, Ulmer A, Detering-Hübner B, Kern P, Schubert F, Dehn G, Schreiber M, Güler C, Schinkel CJ, Gunsenheimer-Bartmeyer B, Schmidt D, Meixenberger K, Bannert N, Wolthers KC, Peters EJG, van Agtmael MA, Autar RS, Bomers M, Sigaloff KCE, Heitmuller M, Laan LM, Ang CW, van Houdt R, Jonges M, Kuijpers TW, Pajkrt D, Scherpbier HJ, de Boer C, van der Plas A, van den Berge M, Stegeman A, Baas S, Hage de Looff L, Buiting A, Reuwer A, Veenemans J, Wintermans B, Pronk MJH, Ammerlaan HSM, van den Bersselaar DNJ, de Munnik ES, Deiman B, Jansz AR, Scharnhorst V, Tjhie J, Wegdam MCA, van Eeden A, Nellen J, Brokking W, Elsenburg LJM, Nobel H, van Kasteren MEE, Berrevoets MAH, Brouwer AE, Adams A, van Erve R, de Kruijf-van de Wiel BAFM, Keelan-Phaf S, van de Ven B, van der Ven B, Buiting AGM, Murck JL, de Vries-Sluijs TEMS, Bax HI, van Gorp ECM, de Jong-Peltenburg NC, de Mendonç A Melo M, van Nood E, Nouwen JL, Rijnders BJA, Rokx C, Schurink CAM, Slobbe L, Verbon A, Bassant N, van Beek JEA, Vriesde M, van Zonneveld LM, de Groot J, Boucher CAB, Koopmans MPG, van Kampen JJA, Fraaij PLA, van Rossum AMC, Vermont CL, van der Knaap LC, Visser E, Branger J, Douma RA, Cents-Bosma AS, Duijf-van de Ven CJHM, Schippers EF, van Nieuwkoop C, van Ijperen JM, Geilings J, van der Hut G, van Burgel ND, Leyten EMS, Gelinck LBS, Mollema F, Davids-Veldhuis S, Tearno C, Wildenbeest GS, Heikens E, Groeneveld PHP, Bouwhuis JW, Lammers AJJ, Kraan S, van Hulzen AGW, Kruiper MSM, van der Bliek GL, Bor PCJ, Debast SB, Wagenvoort GHJ, Kroon FP, de Boer MGJ, Jolink H, Lambregts MMC, Roukens AHE, Scheper H, Dorama W, van Holten N, Claas ECJ, Wessels E, den Hollander JG, El Moussaoui R, Pogany K, Brouwer CJ, Smit JV, Struik-Kalkman D, van Niekerk T, Pontesilli O, Lowe SH, Oude Lashof AML, Posthouwer D, van Wolfswinkel ME, Ackens RP, Burgers K, Schippers J, Weijenberg-Maes B, van Loo IHM, Havenith TRA, van Vonderen MGA, Kampschreur LM, Faber S, Steeman-Bouma R, Al Moujahid A, Kootstra GJ, Delsing CE, van der Burg-van de Plas M, Scheiberlich L, Kortmann W, van Twillert G, Renckens R, Ruiter-Pronk D, van Truijen-Oud FA, Cohen Stuart JWT, Jansen ER, Hoogewerf M, Rozemeijer W, van der Reijden WA, Sinnige JC, Brinkman K, van den Berk GEL, Blok WL, Lettinga KD, de Regt M, Schouten WEM, Stalenhoef JE, Veenstra J, Vrouenraets SME, Blaauw H, Geerders GF, Kleene MJ, Kok M, Knapen M, van der Meché IB, Mulder-Seeleman E, Toonen AJM, Wijnands S, Wttewaal E, Kwa D, van Crevel R, van Aerde K, Dofferhoff ASM, Henriet SSV, Ter Hofstede HJM, Hoogerwerf J, Keuter M, Richel O, Albers M, Grintjes-Huisman KJT, de Haan M, Marneef M, Strik-Albers R, Rahamat-Langendoen J, Stelma FF, Burger D, Gisolf EH, Hassing RJ, Claassen M, Ter Beest G, van Bentum PHM, Langebeek N, Tiemessen R, Swanink CMA, van Lelyveld SFL, Soetekouw R, van der Prijt LMM, van der Swaluw J, Bermon N, van der Reijden WA, Jansen R, Herpers BL, Veenendaal D, Verhagen DWM, Lauw FN, van Broekhuizen MC, van Wijk M, Bierman WFW, Bakker M, Kleinnijenhuis J, Kloeze E, Middel A, Postma DF, Schölvinck EH, Stienstra Y, Verhage AR, Wouthuyzen-Bakker M, Boonstra A, de Groot-de Jonge H, van der Meulen PA, de Weerd DA, Niesters HGM, van Leer-Buter CC, Knoester M, Hoepelman AIM, Arends JE, Barth RE, Bruns AHW, Ellerbroek PM, Mudrikova T, Oosterheert JJ, Schadd EM, van Welzen BJ, Aarsman K, Griffioen-van Santen BMG, de Kroon I, van Berkel M, van Rooijen CSAM, Schuurman R, Verduyn-Lunel F, Wensing AMJ, Bont LJ, Geelen SPM, Loeffen YGT, Wolfs TFW, Nauta N, Rooijakkers EOW, Holtsema H, Voigt R, van de Wetering D, Alberto A, van der Meer I, Rosingh A, Halaby T, Zaheri S, Boyd AC, Bezemer DO, van Sighem AI, Smit C, Hillebregt M, de Jong A, Woudstra T, Bergsma D, Meijering R, van de Sande L, Rutkens T, van der Vliet S, de Groot L, van den Akker M, Bakker Y, El Berkaoui A, Bezemer M, Brétin N, Djoechro E, Groters M, Kruijne E, Lelivelt KJ, Lodewijk C, Lucas E, Munjishvili L, Paling F, Peeck B, Ree C, Regtop R, Ruijs Y, Schoorl M, Schnörr P, Scheigrond A, Tuijn E, Veenenberg L, Visser KM, Witte EC, Ruijs Y, Van Frankenhuijsen M, Allegre T, Makhloufi D, Livrozet JM, Chiarello P, Godinot M, Brunel-Dalmas F, Gibert S, Trepo C, Peyramond D, Miailhes P, Koffi J, Thoirain V, Brochier C, Baudry T, Pailhes S, Lafeuillade A, Philip G, Hittinger G, Assi A, Lambry V, Rosenthal E, Naqvi A, Dunais B, Cua E, Pradier C, Durant J, Joulie A, Quinsat D, Tempesta S, Ravaux I, Martin IP, Faucher O, Cloarec N, Champagne H, Pichancourt G, Morlat P, Pistone T, Bonnet F, Mercie P, Faure I, Hessamfar M, Malvy D, Lacoste D, Pertusa MC, Vandenhende MA, Bernard N, Paccalin F, Martell C, Roger-Schmelz J, Receveur MC, Duffau P, Dondia D, Ribeiro E, Caltado S, Neau D, Dupont M, Dutronc H, Dauchy F, Cazanave C, Vareil MO, Wirth G, Le Puil S, Pellegrin JL, Raymond I, Viallard JF, Chaigne de Lalande S, Garipuy D, Delobel P, Obadia M, Cuzin L, Alvarez M, Biezunski N, Porte L, Massip P, Debard A, Balsarin F, Lagarrigue M, Prevoteau du Clary F, Aquilina C, Reynes J, Baillat V, Merle C, Lemoing V, Atoui N, Makinson A, Jacquet JM, Psomas C, Tramoni C, Aumaitre H, Saada M, Medus M, Malet M, Eden A, Neuville S, Ferreyra M, Sotto A, Barbuat C, Rouanet I, Leureillard D, Mauboussin JM, Lechiche C, Donsesco R, Cabie A, Abel S, Pierre-Francois S, Batala AS, Cerland C, Rangom C, Theresine N, Hoen B, Lamaury I, Fabre I, Schepers K, Curlier E, Ouissa R, Gaud C, Ricaud C, Rodet R, Wartel G, Sautron C, Beck-Wirth G, Michel C, Beck C, Halna JM, Kowalczyk J, Benomar M, Drobacheff-Thiebaut C, Chirouze C, Faucher JF, Parcelier F, Foltzer A, Haffner-Mauvais C, Hustache Mathieu M, Proust A, Piroth L, Chavanet P, Duong M, Buisson M, Waldner A, Mahy S, Gohier S, Croisier D, May T, Delestan M, Andre M, Zadeh MM, Martinot M, Rosolen B, Pachart A, Martha B, Jeunet N, Rey D, Cheneau C, Partisani M, Priester M, Bernard-Henry C, Batard ML, Fischer P, Berger JL, Kmiec I, Robineau O, Huleux T, Ajana F, Alcaraz I, Allienne C, Baclet V, Meybeck A, Valette M, Viget N, Aissi E, Biekre R, Cornavin P, Merrien D, Seghezzi JC, Machado M, Diab G, Raffi F, Bonnet B, Allavena C, Grossi O, Reliquet V, Billaud E, Brunet C, Bouchez S, Morineau-Le Houssine P, Sauser F, Boutoille D, Besnier M, Hue H, Hall N, Brosseau D, Souala F, Michelet C, Tattevin P, Arvieux C, Revest M, Leroy H, Chapplain JM, Dupont M, Fily F, Patra-Delo S, Lefeuvre C, Bernard L, Bastides F, Nau P, Verdon R, de la Blanchardiere A, Martin A, Feret P, Geffray L, Daniel C, Rohan J, Fialaire P, Chennebault JM, Rabier V, Abgueguen P, Rehaiem S, Luycx O, Niault M, Moreau P, Poinsignon Y, Goussef M, Mouton-Rioux V, Houlbert D, Alvarez-Huve S, Barbe F, Haret S, Perre P, Leantez-Nainville S, Esnault JL, Guimard T, Suaud I, Girard JJ, Simonet V, Debab Y, Schmit JL, Jacomet C, Weinberck P, Genet C, Pinet P, Ducroix S, Durox H, Denes É, Abraham B, Gourdon F, Antoniotti O, Molina JM, Ferret S, Lascoux-Combe C, Lafaurie M, Colin de Verdiere N, Ponscarme D, De Castro N, Aslan A, Rozenbaum W, Pintado C, Clavel F, Taulera O, Gatey C, Munier AL, Gazaigne S, Penot P, Conort G, Lerolle N, Leplatois A, Balausine S, Delgado J, Timsit J, Tabet M, Gerard L, Girard PM, Picard O, Tredup J, Bollens D, Valin N, Campa P, Bottero J, Lefebvre B, Tourneur M, Fonquernie L, Wemmert C, Lagneau JL, Yazdanpanah Y, Phung B, Pinto A, Vallois D, Cabras O, Louni F, Pialoux G, Lyavanc T, Berrebi V, Chas J, Lenagat S, Rami A, Diemer M, Parrinello M, Depond A, Salmon D, Guillevin L, Tahi T, Belarbi L, Loulergue P, Zak Dit Zbar O, Launay O, Silbermann B, Leport C, Alagna L, Pietri MP, Simon A, Bonmarchand M, Amirat N, Pichon F, Kirstetter M, Katlama C, Valantin MA, Tubiana R, Caby F, Schneider L, Ktorza N, Calin R, Merlet A, Ben Abdallah S, Weiss L, Buisson M, Batisse D, Karmochine M, Pavie J, Minozzi C, Jayle D, Castel P, Derouineau J, Kousignan P, Eliazevitch M, Pierre I, Collias L, Viard JP, Gilquin J, Sobel A, Slama L, Ghosn J, Hadacek B, Thu-Huyn N, Nait-Ighil L, Cros A, Maignan A, Duvivier C, Consigny PH, Lanternier F, Shoai-Tehrani M, Touam F, Jerbi S, Bodard L, Jung C, Goujard C, Quertainmont Y, Duracinsky M, Segeral O, Blanc A, Peretti D, Cheret A, Chantalat C, Dulucq MJ, Levy Y, Lelievre JD, Lascaux AS, Dumont C, Boue F, Chambrin V, Abgrall S, Kansau I, Raho-Moussa M, De Truchis P, Dinh A, Davido B, Marigot D, Berthe H, Devidas A, Chevojon P, Chabrol A, Agher N, Lemercier Y, Chaix F, Turpault I, Bouchaud O, Honore P, Rouveix E, Reimann E, Belan AG, Godin Collet C, Souak S, Mortier E, Bloch M, Simonpoli AM, Manceron V, Cahitte I, Hiraux E, Lafon E, Cordonnier F, Zeng AF, Zucman D, Majerholc C, Bornarel D, Uludag A, Gellen-Dautremer J, Lefort A, Bazin C, Daneluzzi V, Gerbe J, Jeantils V, Coupard M, Patey O, Bantsimba J, Delllion S, Paz PC, Cazenave B, Richier L, Garrait V, Delacroix I, Elharrar B, Vittecoq D, Bolliot C, Lepretre A, Genet P, Masse V, Perrone V, Boussard JL, Chardon P, Froguel E, Simon P, Tassi S, Avettand Fenoel V, Barin F, Bourgeois C, Cardon F, Chaix ML, Delfraissy JF, Essat A, Fischer H, Lecuroux C, Meyer L, Petrov-Sanchez V, Rouzioux C, Saez-Cirion A, Seng R, Kuldanek K, Mullaney S, Young C, Zucchetti A, Bevan MA, McKernan S, Wandolo E, Richardson C, Youssef E, Green P, Faulkner S, Faville R, Herman S, Care C, Blackman H, Bellenger K, Fairbrother K, Phillips A, Babiker A, Delpech V, Fidler S, Clarke M, Fox J, Gilson R, Goldberg D, Hawkins D, Johnson A, Johnson M, McLean K, Nastouli E, Post F, Kennedy N, Pritchard J, Andrady U, Rajda N, Donnelly C, McKernan S, Drake S, Gilleran G, White D, Ross J, Harding J, Faville R, Sweeney J, Flegg P, Toomer S, Wilding H, Woodward R, Dean G, Richardson C, Perry N, Gompels M, Jennings L, Bansaal D, Browing M, Connolly L, Stanley B, Estreich S, Magdy A, O'Mahony C, Fraser P, Jebakumar SPR, David L, Mette R, Summerfield H, Evans M, White C, Robertson R, Lean C, Morris S, Winter A, Faulkner S, Goorney B, Howard L, Fairley I, Stemp C, Short L, Gomez M, Young F, Roberts M, Green S, Sivakumar K, Minton J, Siminoni A, Calderwood J, Greenhough D, DeSouza C, Muthern L, Orkin C, Murphy S, Truvedi M, McLean K, Hawkins D, Higgs C, Moyes A, Antonucci S, McCormack S, Lynn W, Bevan M, Fox J, Teague A, Anderson J, Mguni S, Post F, Campbell L, Mazhude C, Russell H, Gilson R, Carrick G, Ainsworth J, Waters A, Byrne P, Johnson M, Fidler S, Kuldanek K, Mullaney S, Lawlor V, Melville R, Sukthankar A, Thorpe S, Murphy C, Wilkins E, Ahmad S, Green P, Tayal S, Ong E, Meaden J, Riddell L, Loay D, Peacock K, Blackman H, Harindra V, Saeed AM, Allen S, Natarajan U, Williams O, Lacey H, Care C, Bowman C, Herman S, Devendra SV, Wither J, Bridgwood A, Singh G, Bushby S, Kellock D, Young S, Rooney G, Snart B, Currie J, Fitzgerald M, Arumainayyagam J, Chandramani S. A highly virulent variant of HIV-1 circulating in the Netherlands. Science 2022; 375:540-545. [PMID: 35113714 DOI: 10.1126/science.abk1688] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log10 increase (i.e., a ~3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited CD4 cell decline twice as fast as, 6604 individuals with other subtype-B strains. Without treatment, advanced HIV-CD4 cell counts below 350 cells per cubic millimeter, with long-term clinical consequences-is expected to be reached, on average, 9 months after diagnosis for individuals in their thirties with this variant. Age, sex, suspected mode of transmission, and place of birth for the aforementioned 109 individuals were typical for HIV-positive people in the Netherlands, which suggests that the increased virulence is attributable to the viral strain. Genetic sequence analysis suggests that this variant arose in the 1990s from de novo mutation, not recombination, with increased transmissibility and an unfamiliar molecular mechanism of virulence.
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Affiliation(s)
- Chris Wymant
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,IAME, UMR 1137, INSERM, Université de Paris, Paris, France
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Margreet Bakker
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariateresa de Cesare
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - George MacIntyre-Cockett
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Lucie Abeler-Dörner
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Norbert Bannert
- Division for HIV and Other Retroviruses, Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - M Kate Grabowski
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | | | - Huldrych F Günthard
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Pia Kivelä
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | - Roger D Kouyos
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | | | - Laurence Meyer
- INSERM CESP U1018, Université Paris Saclay, APHP, Service de Santé Publique, Hôpital de Bicêtre, Le Kremlin-Bicêtre, France
| | - Kholoud Porter
- Institute for Global Health, University College London, London, UK
| | - Matti Ristola
- Department of Infectious Diseases, Helsinki University Hospital, Helsinki, Finland
| | | | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Paul Kellam
- Kymab Ltd., Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marion Cornelissen
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Molecular Diagnostic Unit, Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Reiss
- Stichting HIV Monitoring, Amsterdam, Netherlands.,Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam and Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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5
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Tachbele E, Kyobe S, Katabazi FA, Kigozi E, Mwesigwa S, Joloba M, Messele A, Amogne W, Legesse M, Pieper R, Ameni G. Genetic Diversity and Acquired Drug Resistance Mutations Detected by Deep Sequencing in Virologic Failures among Antiretroviral Treatment Experienced Human Immunodeficiency Virus-1 Patients in a Pastoralist Region of Ethiopia. Infect Drug Resist 2021; 14:4833-4847. [PMID: 34819737 PMCID: PMC8607991 DOI: 10.2147/idr.s337485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/03/2021] [Indexed: 01/15/2023] Open
Abstract
Purpose This study was conducted to investigate the drug resistance mutations and genetic diversity of HIV-1 in ART experienced patients in South Omo, Ethiopia. Patients and Methods A cross-sectional study conducted on 253 adult patients attending ART clinics for ≥6 months in South Omo. Samples with VL ≥1000 copies/mL were considered as virological failures (VF) and their reverse transcriptase gene codons 90–234 were sequenced using Illumina MiSeq. MinVar was used for the identification of the subtypes and drug resistance mutations. Phylogenetic tree was constructed by neighbor-joining method using the maximum likelihood model. Results The median duration of ART was 51 months and 18.6% (47/253) of the patients exhibited VF. Of 47 viraemic patients, the genome of 41 were sequenced and subtype C was dominant (87.8%) followed by recombinant subtype BC (4.9%), M-09-CPX (4.9) and BF1 (2.4%). Of 41 genotyped subjects, 85.4% (35/41) had at least one ADR mutation. Eighty-one percent (33/41) of viraemic patients harbored NRTI resistance mutations, and 48.8% (20/41) were positive for NNRTI resistance mutations, with 43.9% dual resistance mutations. Among NRTI resistance mutations, M184V (73.2%), K219Q (63.4%) and T215 (56.1%) complex were the most mutated positions, while the most common NNRTI resistance mutations were K103N (24.4%), K101E, P225H and V108I 7.5% each. Active tuberculosis (aOR=13, 95% CI= 3.46–29.69), immunological failure (aOR=3.61, 95% CI=1.26–10.39), opportunistic infections (aOR=8.39, 95% CI= 1.75–40.19), and poor adherence were significantly associated with virological failure, while rural residence (aOR 2.37; 95% CI: 1.62–9.10, P= 0.05), immunological failures (aOR 2.37; 95% CI: 1.62–9.10, P= 0.05) and high viral load (aOR 16; 95% CI: 5.35 51.59, P <0.001) were predictors of ADR mutation among the ART experienced and viraemic study subjects. Conclusion The study revealed considerable prevalence of VF and ADR mutation with the associated risk indicators. Regular virological monitoring and drug resistance genotyping methods should be implemented for better ART treatment outcomes of the nation.
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Affiliation(s)
- Erdaw Tachbele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.,College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Edgar Kigozi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Moses Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wondwossen Amogne
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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6
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Development of Human Immunodeficiency Virus Type 1 Resistance to 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (EFdA) Starting with Wild-Type or Nucleoside Reverse Transcriptase Inhibitor Resistant-Strains. Antimicrob Agents Chemother 2021; 65:e0116721. [PMID: 34516245 DOI: 10.1128/aac.01167-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA, MK-8591, islatravir) is a nucleoside reverse transcriptase translocation inhibitor (NRTTI) with exceptional potency against WT and drug-resistant HIV-1, in Phase III clinical trials. EFdA resistance is not well characterized. To study EFdA-resistance patterns as it may emerge in naïve or tenofovir- (TFV), emtricitabine/lamivudine- (FTC/3TC), or zidovudine- (AZT) treated patients we performed viral passaging experiments starting with wild-type, K65R, M184V, or D67N/K70R/T215F/K219Q HIV-1. Regardless the starting viral sequence, all selected EFdA-resistant variants included the M184V RT mutation. Using recombinant viruses, we validated the role for M184V as the primary determinant of EFdA resistance; none of the observed connection subdomain (R358K and E399K) or RNase H domain (A502V) mutations significantly contributed to EFdA resistance. A novel EFdA resistance mutational pattern that included A114S was identified in the background of M184V. A114S/M184V exhibited higher EFdA resistance (∼24-fold) than M184V (∼8-fold) or A114S alone (∼2-fold). Remarkably, A114S/M184V and A114S/M184V/A502V resistance mutations were up to 50-fold more sensitive to tenofovir than WT HIV-1. These mutants also had significantly lower specific infectivity than WT. Biochemical experiments confirmed decreases in the enzymatic efficiency (kcat/Km) of WT vs. A114S (2.1-fold) and A114S/M184V/A502V (6.5-fold) RTs, with no effect of A502V on enzymatic efficiency or specific infectivity. The rather modest EFdA resistance of M184V or A114S/M184V (8- and 24-fold), their hypersusceptibility to tenofovir, and strong published in vitro and in vivo data, suggest that EFdA is an excellent therapeutic candidate for naïve, AZT-, FTC/3TC, and especially tenofovir-treated patients.
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7
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Affiliation(s)
- Annette H Sohn
- TREAT Asia, amfAR - The Foundation for AIDS Research, Bangkok, Thailand
| | | | - Peter Reiss
- Department of Global Health, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Institute for Global Health and Development, and HIV Monitoring Foundation, Amsterdam, The Netherlands
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8
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Bianculli RH, Mase JD, Schulz MD. Antiviral Polymers: Past Approaches and Future Possibilities. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01273] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Rachel H. Bianculli
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jonathan D. Mase
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Michael D. Schulz
- Department of Chemistry, Macromolecules Innovation Institute (MII), Virginia Tech, Blacksburg, Virginia 24061, United States
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9
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Bruun L, Katzenstein T, Gerstoft J, Pedersen C, Mathiesen LR, Nielsen C. Development of Lys to Arg Mutation at Codon 70 of the Reverse Transcriptase Gene of HIV-1 during Zidovudine Monotherapy and Alternating Zidovudine/Didanosine Therapy. Antivir Ther 2020. [DOI: 10.1177/135965359800300202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objective To study the association between the Lys to Arg mutation at codon 70 of the reverse transcriptase (RT) gene and resistance development during zidovudine monotherapy and alternating zidovudine/didanosine therapy. Methods Blood samples from 33 antiretroviral-naive patients were drawn prior to therapy and after 6, 12, 18 and 24 months (18 patients received zidovudine monotherapy and 15 patients alternating zidovudine/didanosine). Results: After 6 months of zidovudine monotherapy, 72% of the patients had provirus encoding Lys to Arg at codon 70. This decreased to 53% and 38% after 12 and 18 months, respectively, but increased to 60% after 24 months. During alternating zidovudine/didanosine therapy, the percentages with the mutation were 6%, 7%, 11% and 20% after 6, 12, 18 and 24 months of therapy, respectively. During both therapy regimens provirus showed the same progression of mutations in RT codons 41 and 215, increasing from 10% after 6 months to 80–100% after 24 months. Codon 70 and 215 mutations together were only found with the codon 67 mutation. No significant difference in IC50 or viral load was shown between patients on either therapy. Conclusions The codon 70 mutation was present in a low proportion of the patients during alternating zidovudine/didanosine therapy compared with patients on zidovudine monotherapy ( P<0.01). Mutations associated with zidovudine resistance appeared in an ordered manner. Based on the phenotypic susceptibility of the virus isolated, the appearance of the different combinations of mutations could be explained by outgrowth of virus with an increased level of phenotypic resistance.
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Affiliation(s)
- Louise Bruun
- Retrovirus Laboratory, Department of Virology, Statens Serum Institut, Copenhagen
| | | | - Jan Gerstoft
- Department of Infectious Diseases, Rigshospitalet, Copenhagen
| | - Court Pedersen
- Department of Infectious Diseases C, Odense University Hospital, Odense, Denmark
| | - Lars R Mathiesen
- Department of Infectious Diseases C, Odense University Hospital, Odense, Denmark
| | - Claus Nielsen
- Retrovirus Laboratory, Department of Virology, Statens Serum Institut, Copenhagen
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10
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Gass RJA, Shugarts D, Young R, Allen M, Rosandich M, Kuritzkes DR. Emergence of Dual Resistance to Zidovudine and Lamivudine in Clinical HIV-1 Isolates from Patients Receiving Zidovudine/Lamivudine Combination Therapy. Antivir Ther 2020. [DOI: 10.1177/135965359800300204] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Susceptibility to zidovudine and lamivudine was determined on human immunodeficiency virus type 1 (HIV-1) isolates obtained from patients who added lamivudine after 6 months of treatment with zidovudine. Lamivudine-resistant isolates that were also zidovudine-resistant were recovered from 13/16 (81%) patients after 6 months of dual therapy. In contrast to findings in anti-retroviral therapy-naive patients, these results suggest that dual resistance to zidovudine and lamivudine emerges relatively quickly when lamivudine is added to zidovudine as a single agent in the majority of patients with extensive prior zidovudine treatment.
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Affiliation(s)
- Rebekah JA Gass
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Dave Shugarts
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Russell Young
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Michael Allen
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Mary Rosandich
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
| | - Daniel R Kuritzkes
- University of Colorado Health Sciences Center, Division of Infectious Diseases, and Veterans Affairs Medical Center, Denver, Colorado, USA
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11
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Gibson RM, Nickel G, Crawford M, Kyeyune F, Venner C, Nankya I, Nabulime E, Ndashimye E, Poon AFY, Salata RA, Kityo C, Mugyenyi P, Quiñones-Mateu ME, Arts EJ. Sensitive detection of HIV-1 resistance to Zidovudine and impact on treatment outcomes in low- to middle-income countries. Infect Dis Poverty 2017; 6:163. [PMID: 29202874 PMCID: PMC5716384 DOI: 10.1186/s40249-017-0377-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
Background Thymidine analogs, namely AZT (Zidovudine or Retrovir™) and d4T (Stavudine or Zerit™) are antiretroviral drugs still employed in over 75% of first line combination antiretroviral therapy (cART) in Kampala, Uganda despite aversion to prescribing these drugs for cART in high income countries due in part to adverse events. For this study, we explored how the continued use of these thymidine analogs in cART could impact emergence of drug resistance and impact on future treatment success in Uganda, a low-income country. Methods We examined the drug resistance genotypes by Sanger sequencing of 262 HIV-infected patients failing a first line combined antiretroviral treatment containing either AZT or d4T, which represents approximately 5% of the patients at the Joint Clinical Research Center receiving a AZT or d4T containing treatment. Next generation sequencing (DEEPGEN™HIV) and multiplex oligonucleotide ligation assays (AfriPOLA) were then performed on a subset of patient samples to detect low frequency drug resistant mutations. CD4 cell counts, viral RNA loads, and treatment changes were analyzed in a cohort of treatment success and failures. Results Over 80% of patients failing first line AZT/d4T-containing cART had predicted drug resistance to 3TC (Lamivudine) and non-nucleoside RT inhibitors (NNRTIs) in the treatment regimen but only 45% had resistance AZT/d4T associated resistance mutations (TAMs). TAMs were however detected at low frequency within the patients HIV quasispecies (1–20%) in 21 of 34 individuals who were failing first-line AZT-containing cART and lacked TAMs by Sanger. Due to lack of TAMs by Sanger, AZT was typically maintained in second-line therapies and these patients had a low frequency of subsequent virologic success. Conclusions Our findings suggest that continued use of AZT and d4T in first-line treatment in low-to-middle income countries may lead to misdiagnosis of HIV-1 drug resistance and possibly enhance a succession of second- and third-line treatment failures. Electronic supplementary material The online version of this article (doi: 10.1186/s40249-017-0377-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard M Gibson
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Gabrielle Nickel
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Michael Crawford
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Fred Kyeyune
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Colin Venner
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada
| | - Immaculate Nankya
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda.,Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Eva Nabulime
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Emmanuel Ndashimye
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, University of Western Ontario, Kampala, Uganda
| | - Robert A Salata
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Cissy Kityo
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Peter Mugyenyi
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Miguel E Quiñones-Mateu
- Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, 1151 Richmond St., Dental Sciences Bldg., Rm 3014, London, Ontario, N6A 5C1, Canada. .,TREAT, Joint Clinical Research Centre, Kampala, Uganda.
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12
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Li A, Ziehr JL, Johnson KA. A new general method for simultaneous fitting of temperature and concentration dependence of reaction rates yields kinetic and thermodynamic parameters for HIV reverse transcriptase specificity. J Biol Chem 2017; 292:6695-6702. [PMID: 28255091 DOI: 10.1074/jbc.m116.760827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/21/2017] [Indexed: 11/06/2022] Open
Abstract
Recent studies have demonstrated the dominant role of induced fit in enzyme specificity of HIV reverse transcriptase and many other enzymes. However, relevant thermodynamic parameters are lacking, and equilibrium thermodynamic methods are of no avail because the key parameters can only be determined by kinetic measurement. By modifying KinTek Explorer software, we present a new general method for globally fitting data collected over a range of substrate concentrations and temperatures and apply it to HIV reverse transcriptase. Fluorescence stopped-flow methods were used to record the kinetics of enzyme conformational changes that monitor nucleotide binding and incorporation. The nucleotide concentration dependence was measured at temperatures ranging from 5 to 37 °C, and the raw data were fit globally to derive a single set of rate constants at 37 °C and a set of activation enthalpy terms to account for the kinetics at all other temperatures. This comprehensive analysis afforded thermodynamic parameters for nucleotide binding (Kd , ΔG, ΔH, and ΔS at 37 °C) and kinetic parameters for enzyme conformational changes and chemistry (rate constants and activation enthalpy). Comparisons between wild-type enzyme and a mutant resistant to nucleoside analogs used to treat HIV infections reveal that the ground state binding is weaker and the activation enthalpy for the conformational change step is significantly larger for the mutant. Further studies to explore the structural underpinnings of the observed thermodynamics and kinetics of the conformational change step may help to design better analogs to treat HIV infections and other diseases. Our new method is generally applicable to enzyme and chemical kinetics.
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Affiliation(s)
- An Li
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
| | - Jessica L Ziehr
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
| | - Kenneth A Johnson
- From the Institute for Cell and Molecular Biology, Molecular Biosciences Department, University of Texas at Austin, Austin, Texas 78712
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13
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Cinatl J, Gröschel B, Zehner R, Cinatl J, Périgaud C, Gosselin G, Imbach JL, Doerr HW. Human Immunodeficiency Virus Resistance to AZT in MOLT4/8 Cells is Associated with a Lack of AZT Phosphorylation and is Bypassed by AZT-Monophosphate SATE Prodrugs. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800407] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human T lymphoid MOLT4/8 cells were grown continuously for more than 2 years in a medium containing 3′-azido-2′,3′-dideoxythymidine (zidovudine; AZT) at a concentration of 250 μM. These cells, designated MOLT-4/8rAZT250, were used to test the cytotoxic and antiviral activity of AZT. Intracellular accumulation of AZT, expression of the multidrug resistance 1 (MDR-1) gene, thymidine kinase (TK) gene and activity of the TK enzyme in cellular extracts were measured. The results showed that both the cytotoxic and antiviral activity of AZT were significantly lower in MOLT4/8rAZT250 than in MOLT4/8 cells; concentrations required to inhibit 50% production of the p24 human immunodeficiency virus type 1 (HIV-1) antigen of two laboratory strains were at least 100-fold higher in resistant cells. The MDR-1 gene was not expressed in the resistant cells. TK mRNA expression was significantly lower in the resistant than in the sensitive cells. TK enzymatic activity for deoxythymidine phosphorylation was impaired in MOLT4/8rAZT250 cells compared to the sensitive cells. AZT was phosphorylated only in the sensitive cells whereas no phosphorylation of AZT was found in the resistant cells. We tested whether several AZT-monophosphate triesters, which bypass cellular TK, could overcome resistance to the cytotoxic and antiviral activity of AZT. The bis( t-butylSATE) phosphotriester derivative of AZT showed comparable cytotoxic and antiviral activity in sensitive and resistant cells. The results demonstrated that MOLT4/8rAZT250 cells exert resistance to the anti-HIV activity of the drug mainly owing to the lack of AZT phosphorylation and that resistance may be bypassed by using AZT-monophosphate SATE prodrugs.
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Affiliation(s)
- J Cinatl
- Institut für Medizinische Virologie, Universitätsklinikum, JW Goethe-Universität, Paul-Ehrlich-Strasse 40, D-60596 Frankfurt am Main, Germany
| | - B Gröschel
- Institut für Medizinische Virologie, Universitätsklinikum, JW Goethe-Universität, Paul-Ehrlich-Strasse 40, D-60596 Frankfurt am Main, Germany
| | - R Zehner
- Zentrum der Rechfsmedizin, Universitätsklinikum, JW Goethe-Universität, Kennedyallee 104, D-60596 Frankfurt am Main, Germany
| | - J Cinatl
- Institut für Medizinische Virologie, Universitätsklinikum, JW Goethe-Universität, Paul-Ehrlich-Strasse 40, D-60596 Frankfurt am Main, Germany
- Zentrum für Kinderheilkunde, Abteilung Hämatologie und Onkologie, Universitätsklinikum, JW Goethe-Universität, Theodor-Stern-Kai 7, D-60596 Frankfurt am Main, Germany
| | - C Périgaud
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Courrier 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - G Gosselin
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Courrier 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - J-L Imbach
- Laboratoire de Chimie Bioorganique, UMR CNRS 5625, Case Courrier 008, Université Montpellier II, Sciences et Techniques du Languedoc, Place Eugène Bataillon, 34095 Montpellier, France
| | - HW Doerr
- Institut für Medizinische Virologie, Universitätsklinikum, JW Goethe-Universität, Paul-Ehrlich-Strasse 40, D-60596 Frankfurt am Main, Germany
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14
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Levantis P, Stein C, Oxford J. Molecular and Biological Aspects of AZT Resistant Viruses Derived from HIV-1 Infected Individuals. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029300400301] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- P. Levantis
- Department of Academic Virology, London Hospital Medical College, Turner Street, London E1 2AD, UK
| | - C. Stein
- Department of Academic Virology, London Hospital Medical College, Turner Street, London E1 2AD, UK
| | - J. Oxford
- Department of Academic Virology, London Hospital Medical College, Turner Street, London E1 2AD, UK
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15
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Cox SW, Corrigan G, Palmer S. Inhibition by azidothymidine triphosphate of reverse transcriptase from paired AZT-susceptible and -resistant primary isolates of human immunodeficiency virus type 1. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029500600207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The kinetics and inhibition by 3′-azido-3′-deoxythymidine triphosphate (AZT-TP) of reverse transcriptase (RT) from paired AZT-susceptible and -resistant primary isolates of HIV-1 taken from patients before and after therapy were examined in vitro. The resistant isolates showed mutations in the RT at positions 67, 70, 215 and 219, and also in one case at positions 41 and 215. No changes in the Vmax, the Km for dTTP or the Ki for AZT-TP of a magnitude sufficient to account for the observed development of resistance to AZT in primary isolates from these patients were found.
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Affiliation(s)
- S. W. Cox
- Virology Department, Swedish Institute for Infectious Disease Control, Karolinska Institute, S 105 21 Stockholm, Sweden
| | - G. Corrigan
- Virology Department, Swedish Institute for Infectious Disease Control, Karolinska Institute, S 105 21 Stockholm, Sweden
- Dublin Institute of Technology, Kevin St., Dublin, Republic of Ireland
| | - S. Palmer
- Virology Department, Swedish Institute for Infectious Disease Control, Karolinska Institute, S 105 21 Stockholm, Sweden
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16
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Taylor D, Ahmed S, Brennan T, Navé JF, Casara P, Tyms A. Anti-HIV Activity of MDL 74968, a Novel Acyclonucleotide Derivative of Guanine: Drug Resistance and Drug Combination Effects in Vitro. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029600700505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MDL 74968 (9-[2-methylidene-3-(phosphonomethoxy)-propyl]guanine), a novel acyclonucleotide derivative of guanine, inhibited human immunodeficiency virus type 1 (HIV-1) replication in vitro with activity comparable to that of adefovir (PMEA; 9-(2-phosphonomethoxyethyl)adenine). MDL 74968 was investigated in combination with two licensed nucleoside analogues, zidovudine and didanosine, using a cell viability assay, and drug interactions were evaluated by the isobologram technique, by calculating combination indices and by the MacSynergy™ program. Inhibition of HIV-1 replication was only additive in both cases. MDL 74968 had equivalent antiviral activity against strains of HIV-1 HXB2 engineered to have mutations which conferred resistance to the nucleoside analogues lamivudine, didanosine and zidovudine and the non-nucleoside inhibitor of reverse transcriptase (RT) nevirapine, as against the wild type strain. Continued passage of HIV-1 RF in C8166 cells in the presence of MDL 74968 for 5 months (30 passages) failed to select drug resistant mutants. Continued passage of virus in the presence of the same concentration of adefovir for the same length of time selected a virus in a single culture, which was 3-fold resistant to adefovir and cross-resistant to MDL 74968. Genotypic characterization of this virus revealed a lysine to arginine exchange (AAA to AGA) at position 65 in the RT gene. This virus was not cross-resistant to either zidovudine or nevirapine but showed reduced sensitivity to zalcitabine, didanosine and lamivudine. Continued passage of HIV-1 RF in the presence of nevirapine or zidovudine, using similar experimental protocols selected drug resistant viruses after eight and 17 passages, respectively, but these viruses remained sensitive to adefovir and MDL 74968.
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Affiliation(s)
- D.L. Taylor
- MRC Collaborative Centre, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - S.P. Ahmed
- MRC Collaborative Centre, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - T.M. Brennan
- MRC Collaborative Centre, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - J.-F. Navé
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
| | - P. Casara
- Marion Merrell Dow Research Institute, 16 rue d'Ankara, 67080 Strasbourg Cedex, France
| | - A.S. Tyms
- MRC Collaborative Centre, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
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17
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Palmer S, Cox S. Intracellular Metabolism of 3′-azido-3′-deoxythymidine and 2′,3′-dideoxyinosine in Combination in the Absence and Presence of Ribavirin. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029400500608] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We examined the intracellular phosphorylation of 3′-azido-3′-deoxythymidine (AZT) and 2′,3′-dideoxyinosine (ddl) and the effects on rNTP and dNTP pools when AZT and ddl were incubated separately and in combination in lymphocytes. We also compared the effect of adding ribavirin (RBV) to the two-drug combination of AZT + ddl. AZT and ddl, used singly or in combination, had no effect on the dNTP pools of CEM lymphoblastoid cells. Neither did the combination of AZT + ddl have any effect on the rNTP pools. RBV, a known inhibitor of IMP dehydrogenase, caused a decrease in GTP and an increase in dTTP whether incubated alone or with the drug combination of AZT + ddl. The addition of AZT + ddl therefore did not alter the effects of RBV upon cellular nucleotide pools. AZT was phosphorylated to a much greater extent than ddl. The activation of ddl to ddA-TP was increased 2-fold in the presence of AZT, whereas AZT phosphorylation was unchanged when combined with ddl. This increase in ddl activation may explain in part the synergistic antiviral activity of the combination of AZT + ddl. The increased activation was not due to increased phosphorylation of ddl resulting from IMP dehydrogenase inhibition. The addition of 10 μm RBV to the two-drug combination of AZT + ddl did not change the intracellular phosphorylation of AZT or ddl. The activation of ddl to ddA-TP, when combined with AZT, appeared to be maximal and could not be further increased by addition of RBV to this combination.
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Affiliation(s)
- S. Palmer
- Virology Department, Swedish Institute for Infectious Disease Control, Karolinska Institute, S 105 21 Stockholm, Sweden
- Department of Clinical Virology, Karolinska Institute, Huddinge Hospital F69, S 141 86 Huddinge, Sweden
| | - S. Cox
- Virology Department, Swedish Institute for Infectious Disease Control, Karolinska Institute, S 105 21 Stockholm, Sweden
- Department of Clinical Virology, Karolinska Institute, Huddinge Hospital F69, S 141 86 Huddinge, Sweden
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18
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Analysis of the Zidovudine Resistance Mutations T215Y, M41L, and L210W in HIV-1 Reverse Transcriptase. Antimicrob Agents Chemother 2015; 59:7184-96. [PMID: 26324274 DOI: 10.1128/aac.05069-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 08/23/2015] [Indexed: 01/01/2023] Open
Abstract
Although anti-human immunodeficiency virus type 1 (HIV-1) therapies have become more sophisticated and more effective, drug resistance continues to be a major problem. Zidovudine (azidothymidine; AZT) was the first nucleoside reverse transcriptase (RT) inhibitor (NRTI) approved for the treatment of HIV-1 infections and is still being used, particularly in the developing world. This drug targets the conversion of single-stranded RNA to double-stranded DNA by HIV-1 RT. However, resistance to the drug quickly appeared both in viruses replicating in cells in culture and in patients undergoing AZT monotherapy. The primary resistance pathway selects for mutations of T215 that change the threonine to either a tyrosine or a phenylalanine (T215Y/F); this resistance pathway involves an ATP-dependent excision mechanism. The pseudo-sugar ring of AZT lacks a 3' OH; RT incorporates AZT monophosphate (AZTMP), which blocks the end of the viral DNA primer. AZT-resistant forms of HIV-1 RT use ATP in an excision reaction to unblock the 3' end of the primer strand, allowing its extension by RT. The T215Y AZT resistance mutation is often accompanied by two other mutations, M41L and L210W. In this study, the roles of these mutations, in combination with T215Y, were examined to determine whether they affect polymerization and excision by HIV-1 RT. The M41L mutation appears to help restore the DNA polymerization activity of RT containing the T215Y mutation and also enhances AZTMP excision. The L210W mutation plays a similar role, but it enhances excision by RTs that carry the T215Y mutation when ATP is present at a low concentration.
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19
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HIV-1 subtypes and drug resistance profiles in a cohort of heterosexual patients in Istanbul, Turkey. Med Microbiol Immunol 2015; 204:551-5. [PMID: 25916350 DOI: 10.1007/s00430-015-0419-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/20/2015] [Indexed: 12/23/2022]
Abstract
Turkey is seeing a steady rise in rates of HIV infection in the country. The number of individuals with HIV/AIDS was greater than 7000 in 2014 according to data released by the Ministry of Health, and heterosexual contacts were reported to be the main transmission routes. Istanbul has the highest number of reported cases of HIV infection. The aim of the study was to determine the prevalence of HIV-1 drug resistance in 50 heterosexual patients from Istanbul. The most prevalent subtype was found to be subtype B (56.2 %). Resistance-associated mutations were found in 14 patients with 6/14 patients being therapy-experienced and 8/14 therapy naive at the time point of analysis. With increasing number of patients who require treatment and the rapid up-scaling of the antiretroviral therapy in Turkey, HIV-1 drug resistance testing is recommended before starting treatment in order to achieve better clinical outcomes.
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20
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Telwatte S, Hearps AC, Johnson A, Latham CF, Moore K, Agius P, Tachedjian M, Sonza S, Sluis-Cremer N, Harrigan PR, Tachedjian G. Silent mutations at codons 65 and 66 in reverse transcriptase alleviate indel formation and restore fitness in subtype B HIV-1 containing D67N and K70R drug resistance mutations. Nucleic Acids Res 2015; 43:3256-71. [PMID: 25765644 PMCID: PMC4381058 DOI: 10.1093/nar/gkv128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/06/2015] [Indexed: 01/03/2023] Open
Abstract
Resistance to combined antiretroviral therapy (cART) in HIV-1-infected individuals is typically due to nonsynonymous mutations that change the protein sequence; however, the selection of synonymous or ‘silent’ mutations in the HIV-1 genome with cART has been reported. These silent K65K and K66K mutations in the HIV-1 reverse transcriptase (RT) occur in over 35% of drug-experienced individuals and are highly associated with the thymidine analog mutations D67N and K70R, which confer decreased susceptibility to most nucleoside and nucleotide RT inhibitors. However, the basis for selection of these silent mutations under selective drug pressure is unknown. Using Illumina next-generation sequencing, we demonstrate that the D67N/K70R substitutions in HIV-1 RT increase indel frequency by 100-fold at RT codons 65–67, consequently impairing viral fitness. Introduction of either K65K or K66K into HIV-1 containing D67N/K70R reversed the error-prone DNA synthesis at codons 65–67 in RT and improved viral replication fitness, but did not impact RT inhibitor drug susceptibility. These data provide new mechanistic insights into the role of silent mutations selected during antiretroviral therapy and have broader implications for the relevance of silent mutations in the evolution and fitness of RNA viruses.
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Affiliation(s)
- Sushama Telwatte
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna C Hearps
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Infectious Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - Adam Johnson
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Catherine F Latham
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Katie Moore
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Paul Agius
- Centre for Population Health, Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Mary Tachedjian
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria 3220, Australia
| | - Secondo Sonza
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicolas Sluis-Cremer
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - P Richard Harrigan
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC V6Z1Y6, Canada
| | - Gilda Tachedjian
- Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria 3004, Australia Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia Department of Infectious Diseases, Monash University, Melbourne, Victoria 3004, Australia Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
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Schneider A, Schweimer K, Rösch P, Wöhrl BM. AZT resistance alters enzymatic properties and creates an ATP-binding site in SFVmac reverse transcriptase. Retrovirology 2015; 12:21. [PMID: 25808094 PMCID: PMC4359774 DOI: 10.1186/s12977-015-0147-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The replication of simian foamy virus from macaques can be inhibited by the nucleoside reverse transcriptase inhibitor azidothymidine (AZT, zidovudine). Four substitutions in the protease-reverse transcriptase (PR-RT) protein (K211I, I224T, S345T, E350K) are necessary to obtain highly AZT resistant and fully replication competent virus. AZT resistance is based on the excision of the incorporated AZTMP in the presence of ATP. I224T is a polymorphism which is not essential for AZT resistance per se, but is important for regaining efficient replication of the resistant virus. RESULTS We constructed PR-RT enzymes harboring one to four amino acid substitutions to analyze them biochemically and to determine their ability to remove the incorporated AZTMP. S345T is the only single substitution variant exhibiting significant AZTMP excision activity. Although K211I alone showed no AZTMP excision activity, excision efficiency doubled when K211I was present in combination with S345T and E350K. K211I also decreased nucleotide binding affinity and increased fidelity. NMR titration experiments revealed that a truncated version of the highly AZT resistant mt4 variant, comprising only the fingers-palm subdomains was able to bind ATP with a KD-value of ca. 7.6 mM, whereas no ATP binding could be detected in the corresponding wild type protein. We could show by NMR spectroscopy that S345T is responsible for ATP binding, probably by making a tryptophan residue accessible. CONCLUSION Although AZT resistance in SFVmac is based on excision of the incorporated AZTMP like in HIV-1, the functions of the resistance substitutions in SFVmac PR-RT appear to be different. No mutation resulting in an aromatic residue like F/Y215 in HIV, which is responsible for π-π-stacking interactions with ATP, is present in SFVmac. Instead, S345T is responsible for creating an ATP binding site, probably by making an already existing tryptophan more accessible, which in turn can interact with ATP. This is in contrast to HIV-1 RT, in which an ATP binding site is present in the WT RT but differs from that of the AZT resistant enzyme.
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Impact of human immunodeficiency virus type-1 sequence diversity on antiretroviral therapy outcomes. Viruses 2014; 6:3855-72. [PMID: 25333465 PMCID: PMC4213566 DOI: 10.3390/v6103855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/09/2014] [Accepted: 10/13/2014] [Indexed: 12/04/2022] Open
Abstract
Worldwide circulating HIV-1 genomes show extensive variation represented by different subtypes, polymorphisms and drug-resistant strains. Reports on the impact of sequence variation on antiretroviral therapy (ART) outcomes are mixed. In this review, we summarize relevant published data from both resource-rich and resource-limited countries in the last 10 years on the impact of HIV-1 sequence diversity on treatment outcomes. The prevalence of transmission of drug resistant mutations (DRMs) varies considerably, ranging from 0% to 27% worldwide. Factors such as geographic location, access and availability to ART, duration since inception of treatment programs, quality of care, risk-taking behaviors, mode of transmission, and viral subtype all dictate the prevalence in a particular geographical region. Although HIV-1 subtype may not be a good predictor of treatment outcome, review of emerging evidence supports the fact that HIV-1 genome sequence-resulting from natural polymorphisms or drug-associated mutations-matters when it comes to treatment outcomes. Therefore, continued surveillance of drug resistant variants in both treatment-naïve and treatment-experienced populations is needed to reduce the transmission of DRMs and to optimize the efficacy of the current ART armamentarium.
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Vanpouille C, Khandazhinskaya A, Karpenko I, Zicari S, Barreto-de-Souza V, Frolova S, Margolis L, Kochetkov S. A new antiviral: chimeric 3TC-AZT phosphonate efficiently inhibits HIV-1 in human tissues ex vivo. Antiviral Res 2014; 109:125-31. [PMID: 25010891 DOI: 10.1016/j.antiviral.2014.06.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/25/2014] [Accepted: 06/26/2014] [Indexed: 01/18/2023]
Abstract
Although more-recently developed antivirals target different molecules in the HIV-1 replication cycle, nucleoside reverse transcriptase inhibitors (NRTIs) remain central for HIV-1 therapy. Here, we test the anti-HIV activity of a phosphonate chimera of two well-known NRTIs, namely AZT and 3TC. We show that this newly synthesized compound suppressed HIV-1 infection in lymphoid tissue ex vivo more efficiently than did other phosphonates of NRTIs. Moreover, the new compound was not toxic for tissue cells, thus making the chimeric phosphonate strategy a valid approach for the development of anti HIV-1 compound heterodimers.
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Affiliation(s)
- Christophe Vanpouille
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | | | - Inna Karpenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Sonia Zicari
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Victor Barreto-de-Souza
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Svetlana Frolova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Leonid Margolis
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States.
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation.
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Megens S, Vaira D, De Baets G, Dekeersmaeker N, Schrooten Y, Li G, Schymkowitz J, Rousseau F, Vandamme AM, Moutschen M, Van Laethem K. Horizontal gene transfer from human host to HIV-1 reverse transcriptase confers drug resistance and partly compensates for replication deficits. Virology 2014; 456-457:310-8. [DOI: 10.1016/j.virol.2014.03.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 01/24/2014] [Accepted: 03/22/2014] [Indexed: 10/25/2022]
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Abstract
The most significant advance in the medical management of HIV-1 infection has been the treatment of patients with antiviral drugs, which can suppress HIV-1 replication to undetectable levels. The discovery of HIV-1 as the causative agent of AIDS together with an ever-increasing understanding of the virus replication cycle have been instrumental in this effort by providing researchers with the knowledge and tools required to prosecute drug discovery efforts focused on targeted inhibition with specific pharmacological agents. To date, an arsenal of 24 Food and Drug Administration (FDA)-approved drugs are available for treatment of HIV-1 infections. These drugs are distributed into six distinct classes based on their molecular mechanism and resistance profiles: (1) nucleoside-analog reverse transcriptase inhibitors (NNRTIs), (2) non-nucleoside reverse transcriptase inhibitors (NNRTIs), (3) integrase inhibitors, (4) protease inhibitors (PIs), (5) fusion inhibitors, and (6) coreceptor antagonists. In this article, we will review the basic principles of antiretroviral drug therapy, the mode of drug action, and the factors leading to treatment failure (i.e., drug resistance).
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Affiliation(s)
- Eric J Arts
- Ugandan CFAR Laboratories, Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA.
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Molecular epidemiology of HIV in a cohort of men having sex with men from Istanbul. Med Microbiol Immunol 2013; 202:251-5. [PMID: 23296905 DOI: 10.1007/s00430-012-0285-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 12/12/2012] [Indexed: 02/01/2023]
Abstract
In Turkey, the first HIV/AIDS case was reported in 1985. Since then the number of persons with HIV infection has increased, HIV is getting a public health problem. The aim of this study was to determine HIV-1 subtype diversity, drug resistance and gag cleavage site mutations among 20 HIV-infected men having sex with men from Istanbul, Turkey. The most prevalent subtype was found to be subtype B (50 %), but also the non-B subtypes A1, C and CRF02_AG, CRF03_AB and CRF06_cpx were found. Resistance-associated mutations were found in 6 patients (30 %) with 2/6 patients being therapy-experienced and 4/6 therapy-naïve at the time-point of analysis. In these patients, the nucleoside reverse transcriptase inhibitor (NRTI)-associated resistance mutations M41L, T215C, V75I, T69N, the non-NRTI associated mutations V106I, E138A, K103N and the protease inhibitor associated mutations Q58E and V82I were detected. Two virus strains also presented Gag cleavage site mutations. With increasing numbers of HIV-infected Turkish patients that require anti-retroviral treatment, HIV-1 drug-resistance testing is strongly recommended in order to choose the most active drug combination for therapy to achieve better clinical outcomes.
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Khandazhinskaya А, Shirokova E. AZT 5'-Phosphonates: Achievements and Trends in the Treatment and Prevention of HIV Infection. Acta Naturae 2013; 5:54-61. [PMID: 24307936 PMCID: PMC3848067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite the numerous drawbacks, 3'-azido-3'-deoxythymidine (AZT, Zidovudine, Retrovir) remains one of the key drugs used in the treatment and prevention of HIV infection in both monotherapy and HAART. A strategy in searching for new effective and safe AZT agents among latent (depot) forms of AZT has yielded its first positive results. In particular, the sodium salt of AZT 5'-H-phosphonate (Nikavir, phosphazide) has demonstrated clinical advantages over parent AZT: first and foremost, lower toxicity and better tolerability. It can be effectively used for the prevention of vertical transmission from mothers to babies and as an alternative drug for HIV-infected patients with low tolerance to Zidovudine. Preclinical studies of another phosphonate, AZT 5'-aminocarbonylphosphonate, have demonstrated that it releases AZT when taken orally. Pharmacokinetic studies have shown a prolonged action potential. Based on the analysis of both toxicological and pharmacological data, AZT 5'-aminocarbonylphosphonate has been recommended for clinical trials.
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Affiliation(s)
- А.L. Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, Moscow, Russia, 119991
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Brehm JH, Scott Y, Koontz DL, Perry S, Hammer S, Katzenstein D, Mellors JW, Sluis-Cremer N. Zidovudine (AZT) monotherapy selects for the A360V mutation in the connection domain of HIV-1 reverse transcriptase. PLoS One 2012; 7:e31558. [PMID: 22363673 PMCID: PMC3283647 DOI: 10.1371/journal.pone.0031558] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 01/13/2012] [Indexed: 11/19/2022] Open
Abstract
Background We previously demonstrated in vitro that zidovudine (AZT) selects for A371V in the connection domain and Q509L in ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT) which, together with the thymidine analog mutations D67N, K70R and T215F, confer greater than 100-fold AZT resistance. The goal of the current study was to determine whether AZT monotherapy in HIV-1 infected patients also selects the A371V, Q509L or other mutations in the C-terminal domains of HIV-1 RT. Methodology/Principal Findings Full-length RT sequences in plasma obtained pre- and post-therapy were compared in 23 participants who received AZT monotherapy from the AIDS Clinical Trials Group study 175. Five of the 23 participants reached a primary study endpoint. Mutations significantly associated with AZT monotherapy included K70R (p = 0.003) and T215Y (p = 0.013) in the polymerase domain of HIV-1 RT, and A360V (p = 0.041) in the connection domain of HIV-1 RT. HIV-1 drug susceptibility assays demonstrated that A360V, either alone or in combination with thymidine analog mutations, decreased AZT susceptibility in recombinant viruses containing participant-derived full-length RT sequences or site-directed mutant RT. Biochemical studies revealed that A360V enhances the AZT-monophosphate excision activity of purified RT by significantly decreasing the frequency of secondary RNase H cleavage events that reduce the RNA/DNA duplex length and promote template/primer dissociation. Conclusions The A360V mutation in the connection domain of RT was selected in HIV-infected individuals that received AZT monotherapy and contributed to AZT resistance.
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Affiliation(s)
- Jessica H. Brehm
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Yanille Scott
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- Department of Infectious Disease and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania, United States of America
| | - Dianna L. Koontz
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Steven Perry
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Scott Hammer
- Columbia University Medical Center, New York, New York, United States of America
| | - David Katzenstein
- Division of Infectious Diseases, Center for AIDS Research, Stanford, California, United States of America
| | - John W. Mellors
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Nicolas Sluis-Cremer
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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von Kleist M, Metzner P, Marquet R, Schütte C. HIV-1 polymerase inhibition by nucleoside analogs: cellular- and kinetic parameters of efficacy, susceptibility and resistance selection. PLoS Comput Biol 2012; 8:e1002359. [PMID: 22275860 PMCID: PMC3261923 DOI: 10.1371/journal.pcbi.1002359] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 12/05/2011] [Indexed: 11/30/2022] Open
Abstract
Nucleoside analogs (NAs) are used to treat numerous viral infections and cancer. They compete with endogenous nucleotides (dNTP/NTP) for incorporation into nascent DNA/RNA and inhibit replication by preventing subsequent primer extension. To date, an integrated mathematical model that could allow the analysis of their mechanism of action, of the various resistance mechanisms, and their effect on viral fitness is still lacking. We present the first mechanistic mathematical model of polymerase inhibition by NAs that takes into account the reversibility of polymerase inhibition. Analytical solutions for the model point out the cellular- and kinetic aspects of inhibition. Our model correctly predicts for HIV-1 that resistance against nucleoside analog reverse transcriptase inhibitors (NRTIs) can be conferred by decreasing their incorporation rate, increasing their excision rate, or decreasing their affinity for the polymerase enzyme. For all analyzed NRTIs and their combinations, model-predicted macroscopic parameters (efficacy, fitness and toxicity) were consistent with observations. NRTI efficacy was found to greatly vary between distinct target cells. Surprisingly, target cells with low dNTP/NTP levels may not confer hyper-susceptibility to inhibition, whereas cells with high dNTP/NTP contents are likely to confer natural resistance. Our model also allows quantification of the selective advantage of mutations by integrating their effects on viral fitness and drug susceptibility. For zidovudine triphosphate (AZT-TP), we predict that this selective advantage, as well as the minimal concentration required to select thymidine-associated mutations (TAMs) are highly cell-dependent. The developed model allows studying various resistance mechanisms, inherent fitness effects, selection forces and epistasis based on microscopic kinetic data. It can readily be embedded in extended models of the complete HIV-1 reverse transcription process, or analogous processes in other viruses and help to guide drug development and improve our understanding of the mechanisms of resistance development during treatment. Nucleoside analogs (NAs) represent an important drug class for the treatment of viral infections and cancer. They inhibit DNA/RNA polymerization after being incorporated into nascent DNA/RNA, which prevents primer extension. Viruses are particularly versatile and frequently develop mutations enabling them to avert the effects of NAs. The mechanisms of resistance development are, however, still poorly understood. Through mathematical modeling, we assess the mechanisms by which HIV-1 can develop resistance against nucleoside analog reverse transcriptase inhibitors (NRTI). We quantify the effects of treatment and estimate the fitness of drug resistant mutants. We correctly predict that HIV-1 can develop resistance by decreasing NRTI incorporation rate, increasing its excision rate, or decreasing its affinity for the viral polymerase enzyme. Our model also allows quantification of the cell specific factors affecting NRTI efficacy. Resistance development also changes drug susceptibility distinctly and we show, for the first time, that selection of drug resistance can occur in particular target cells. This finding could provide an explanation of how clinically observed resistant viral mutants may arise. It also pin-points important parameters that may impact clinical efficacy of NAs used to treat other viruses.
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Affiliation(s)
- Max von Kleist
- Department of Mathematics and Computer Science, Free University Berlin, Berlin, Germany.
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Mizuhara T, Oishi S, Ohno H, Shimura K, Matsuoka M, Fujii N. Concise synthesis and anti-HIV activity of pyrimido[1,2-c][1,3]benzothiazin-6-imines and related tricyclic heterocycles. Org Biomol Chem 2012; 10:6792-802. [DOI: 10.1039/c2ob25904d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Johnson VA, Calvez V, Günthard HF, Paredes R, Pillay D, Shafer R, Wensing AM, Richman DD. 2011 update of the drug resistance mutations in HIV-1. TOPICS IN ANTIVIRAL MEDICINE 2011; 19:156-164. [PMID: 22156218 PMCID: PMC6148877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This November 2011 edition of the IAS-USA drug resistance mutations list updates the figures last published in December 2010 (Johnson VA et al, Top HIV Med, 2010;18:156-163).
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Affiliation(s)
- Victoria A Johnson
- Birmingham Veterans Affairs Medical Center and the University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
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Taylor BS, Hunt G, Abrams EJ, Coovadia A, Meyers T, Sherman G, Strehlau R, Morris L, Kuhn L. Rapid development of antiretroviral drug resistance mutations in HIV-infected children less than two years of age initiating protease inhibitor-based therapy in South Africa. AIDS Res Hum Retroviruses 2011; 27:945-56. [PMID: 21345162 PMCID: PMC3161115 DOI: 10.1089/aid.2010.0205] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Data on the development of antiretroviral drug resistance in HIV-1-infected children receiving protease inhibitor (PI)-based antiretroviral therapy (ART) are limited. We examined antiretroviral resistance among a cohort of 323 South African HIV-infected children <2 years old exposed to nevirapine for prevention of mother-to-child transmission. Ritonavir (RTV) was used initially for 138 children who were <6 months old or receiving antimycobacterial therapy; otherwise children received lopinavir/ritonavir (LPV/r)-based ART. HIV-1 population sequencing of the pol gene was conducted on all pretreatment samples and on posttreatment samples for children who did not achieve HIV-1 plasma RNA <400 copies/ml by 52 weeks. Among children in the cohort, 38 died, 22 had <24 weeks follow-up, 209 achieved virologic suppression, and 54 did not. Of 41 children without virologic suppression with posttreatment HIV genotype data available, major resistance mutations were found in 32 (78%): 14 (36%) had PI mutations including V82A, M46I, and L90M; 29 (71%) had M184V/I; and three had NNRTI mutations (K103N, Y181C, and G190A). Among the children who did not achieve virologic suppression, none of the seven children treated exclusively with LPV/r developed PI-related mutations, compared with 14 of 32 (44%) who received RTV-based regimens (p=0.036); PI genotypes were unavailable for two children. Seventy-eight percent of children without virologic suppression developed resistance mutations that impact second-line ART options. Only children who received RTV-based ART developed major PI-related resistance mutations, and use of this regimen should be avoided.
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Affiliation(s)
- Barbara S. Taylor
- Division of Infectious Diseases, Department of Medicine, University of Texas Health Sciences Center at San Antonio, San Antonio, Texas and College of Physicians and Surgeons, Columbia University Medical Center, New York, New York
| | - Gillian Hunt
- AIDS Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Elaine J. Abrams
- International Center for AIDS Programs, Mailman School of Public Health, Columbia University, New York, New York
| | - Ashraf Coovadia
- Empilweni Services and Research Unit, Rahima Moosa Mothers and Children Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Tammy Meyers
- Harriet Shezi Clinic, Chris Hani Baragwanath Hospital, Enhancing Childhood HIV Outcomes (ECHO), University of the Witwatersrand, Johannesburg, South Africa
| | - Gayle Sherman
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, and National Health Laboratory Service, Johannesburg, South Africa
| | - Renate Strehlau
- Empilweni Services and Research Unit, Rahima Moosa Mothers and Children Hospital, University of the Witwatersrand, Johannesburg, South Africa
| | - Lynn Morris
- AIDS Research Unit, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Louise Kuhn
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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Kisic M, Matamoros T, Nevot M, Mendieta J, Martinez-Picado J, Martínez MA, Menéndez-Arias L. Thymidine analogue excision and discrimination modulated by mutational complexes including single amino acid deletions of Asp-67 or Thr-69 in HIV-1 reverse transcriptase. J Biol Chem 2011; 286:20615-24. [PMID: 21504903 DOI: 10.1074/jbc.m111.226100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Single amino acid deletions in the β3-β4 hairpin loop of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) have been identified in heavily treated patients. The deletion of Asp-67 together with mutations T69G and K70R (Δ67 complex) are usually associated with thymidine analog resistance mutations (TAMs) (e.g. M41L, T215Y, etc.) while the deletion of Thr-69 (Δ69) is rarely found in isolates containing TAMs. Here, we show that the complex Δ67/T69G/K70R enhances ATP-dependent phosphorolytic activity on primers terminated with 3'-azido-3'-deoxythymidine (AZT) or 2',3'-didehydro-2',3'-dideoxythymidine (d4T) both in the presence or absence of TAMs (i.e. M41L/T215Y), while Δ69 (or the complex S68G/Δ69/K70G) antagonize the effects of TAMs in ATP-mediated excision. These effects are consistent with AZT susceptibility data obtained with recombinant HIV-1 bearing the relevant RTs. Molecular dynamics studies based on models of wild-type HIV-1 RT and mutant Δ69, Δ67/T69G/K70R, and D67N/K70R RTs support a relevant role for Lys/Arg-70 in the excision reaction. In Δ69 RT, the side chain of Lys-70 locates away from the putative pyrophosphate binding site. Therefore, its participation in interactions required for the excision reaction is unlikely. Our theoretical studies also suggest a role for Lys-219 in thymidine analog excision/discrimination. However, pre-steady-state kinetics revealed only minor differences in selectivity of AZT-triphosphate versus dTTP between deletion-containing RTs and their homologous enzymes having the K219E mutation. K219E reduced both ATP- and pyrophosphate-mediated excision of primers terminated with thymidine analogues, only when introduced in RTs bearing Δ69 or S68G/Δ69/K70G, providing further biochemical evidence that explains the lack of association of Δ69 and TAMs in HIV-1 isolates.
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Affiliation(s)
- Mónica Kisic
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E. Structural basis of HIV-1 resistance to AZT by excision. Nat Struct Mol Biol 2010; 17:1202-9. [PMID: 20852643 PMCID: PMC2987654 DOI: 10.1038/nsmb.1908] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/20/2010] [Indexed: 02/02/2023]
Abstract
Human immunodeficiency virus (HIV-1) develops resistance to 3'-azido-2',3'-deoxythymidine (AZT, zidovudine) by acquiring mutations in reverse transcriptase that enhance the ATP-mediated excision of AZT monophosphate from the 3' end of the primer. The excision reaction occurs at the dNTP-binding site, uses ATP as a pyrophosphate donor, unblocks the primer terminus and allows reverse transcriptase to continue viral DNA synthesis. The excision product is AZT adenosine dinucleoside tetraphosphate (AZTppppA). We determined five crystal structures: wild-type reverse transcriptase-double-stranded DNA (RT-dsDNA)-AZTppppA; AZT-resistant (AZTr; M41L D67N K70R T215Y K219Q) RT-dsDNA-AZTppppA; AZTr RT-dsDNA terminated with AZT at dNTP- and primer-binding sites; and AZTr apo reverse transcriptase. The AMP part of AZTppppA bound differently to wild-type and AZTr reverse transcriptases, whereas the AZT triphosphate part bound the two enzymes similarly. Thus, the resistance mutations create a high-affinity ATP-binding site. The structure of the site provides an opportunity to design inhibitors of AZT-monophosphate excision.
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Affiliation(s)
- Xiongying Tu
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey, USA
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Khandazhinskaya A, Matyugina E, Shirokova E. Anti-HIV therapy with AZT prodrugs: AZT phosphonate derivatives, current state and prospects. Expert Opin Drug Metab Toxicol 2010; 6:701-14. [DOI: 10.1517/17425251003713501] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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HIV-1 RT Inhibitors with a Novel Mechanism of Action: NNRTIs that Compete with the Nucleotide Substrate. Viruses 2010; 2:880-899. [PMID: 21994659 PMCID: PMC3185657 DOI: 10.3390/v2040880] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 02/20/2010] [Accepted: 03/05/2010] [Indexed: 11/16/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) inhibitors currently used in antiretroviral therapy can be divided into two classes: (i) nucleoside analog RT inhibitors (NRTIs), which compete with natural nucleoside substrates and act as terminators of proviral DNA synthesis, and (ii) non-nucleoside RT inhibitors (NNRTIs), which bind to a hydrophobic pocket close to the RT active site. In spite of the efficiency of NRTIs and NNRTIs, the rapid emergence of multidrug-resistant mutations requires the development of new RT inhibitors with an alternative mechanism of action. Recently, several studies reported the discovery of novel non-nucleoside inhibitors with a distinct mechanism of action. Unlike classical NNRTIs, they compete with the nucleotide substrate, thus forming a new class of RT inhibitors: nucleotide-competing RT inhibitors (NcRTIs). In this review, we discuss current progress in the understanding of the peculiar behavior of these compounds.
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Acosta-Hoyos AJ, Scott WA. The Role of Nucleotide Excision by Reverse Transcriptase in HIV Drug Resistance. Viruses 2010; 2:372-394. [PMID: 20523911 PMCID: PMC2879589 DOI: 10.3390/v2020372] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Revised: 01/15/2010] [Accepted: 01/25/2010] [Indexed: 01/17/2023] Open
Abstract
Nucleoside reverse transcriptase (RT) inhibitors of HIV block viral replication through the ability of HIV RT to incorporate chain-terminating nucleotide analogs during viral DNA synthesis. Once incorporated, the chain-terminating residue must be removed before DNA synthesis can continue. Removal can be accomplished by the excision activity of HIV RT, which catalyzes the transfer of the 3'-terminal residue on the blocked DNA chain to an acceptor substrate, probably ATP in most infected cells. Mutations of RT that enhance excision activity are the most common cause of resistance to 3'-azido-3'-deoxythymidine (AZT) and exhibit low-level cross-resistance to most other nucleoside RT inhibitors. The resistance to AZT is suppressed by a number of additional mutations in RT, most of which were identified because they conferred resistance to other RT inhibitors. Here we review current understanding of the biochemical mechanisms responsible for increased or decreased excision activity due to these mutations.
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Affiliation(s)
- Antonio J. Acosta-Hoyos
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, P.O. Box 016129, Miami, FL 33101-6129, USA; E-Mail: (A.J.A.-H.)
| | - Walter A. Scott
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, P.O. Box 016129, Miami, FL 33101-6129, USA; E-Mail: (A.J.A.-H.)
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Kandathil AJ, Kannangai R, Abraham OC, Rupali P, Pulimood SA, Verghese VP, Grant P, Pillay D, Sridharan G. The frequency of HIV-I drug resistance mutations among treatment-naive individuals at a tertiary care centre in south India. Int J STD AIDS 2009; 20:522-6. [PMID: 19625581 DOI: 10.1258/ijsa.2008.008403] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antiretroviral treatment (ART) use in India requires information on baseline drug resistance mutations and polymorphisms in the protease (Pr) and reverse transcriptase (RT) genes of HIV-1 strains from treatment-naïve individuals. We report resistance predictor mutations and polymorphisms in the Pr and the RT sequence of non-clade B HIV-1 strains from ART naïve individuals. The genotypic resistance assay was done on 93 treatment-naïve individuals. The sequences were analysed by Stanford HIV drug resistance data for genotypic drug resistance analysis and REGA HIV-1 subtyping tool. Phylogenetic tree was generated with MEGA 4 for quality control. Ninety-two strains belonged to clade C and one to clade A (A1). Amino acid substitutions were seen at positions associated with drug resistance in Pr gene--10, 24, 74 (each 3%) and position 82 (11%). Substitutions were seen at positions 41 (1%), 100 (1%), 101 (6%), 103 (2%), 179 (6%) and 181 (1%) of the RT sequence known to confer drug resistance in clade B. Polymorphisms in HIV-1 pol gene among treatment-naïve individuals were similar when compared with previous data. One strain each had Y181C substitution, T74S and E35G substitutions in the Pr and one had A98G, K101R and L210FL substitutions in RT.
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Affiliation(s)
- A J Kandathil
- Department of Clinical Virology, Christian Medical College, Vellore, India
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Margot NA, Enejosa J, Cheng AK, Miller MD, McColl DJ. Development of HIV-1 Drug Resistance Through 144 Weeks in Antiretroviral-Naïve Subjects on Emtricitabine, Tenofovir Disoproxil Fumarate, and Efavirenz Compared With Lamivudine/Zidovudine and Efavirenz in Study GS-01-934. J Acquir Immune Defic Syndr 2009; 52:209-21. [DOI: 10.1097/qai.0b013e3181b05f7c] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Impact of novel human immunodeficiency virus type 1 reverse transcriptase mutations P119S and T165A on 4'-ethynylthymidine analog resistance profile. Antimicrob Agents Chemother 2009; 53:4640-6. [PMID: 19704131 DOI: 10.1128/aac.00686-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2',3'-Didehydro-3'-deoxy-4'-ethynylthymidine (4'-Ed4T), a derivative of stavudine (d4T), has potent activity against human immunodeficiency virus and is much less inhibitory to mitochondrial DNA synthesis and cell growth than its progenitor, d4T. 4'-Ed4T triphosphate was a better reverse transcriptase (RT) inhibitor than d4T triphosphate, due to the additional binding of the 4'-ethynyl group at a presumed hydrophobic pocket in the RT active site. Previous in vitro selection for 4'-Ed4T-resistant viral strains revealed M184V and P119S/T165A/M184V mutations on days 26 and 81, respectively; M184V and P119S/T165A/M184V conferred 3- and 130-fold resistance to 4'-Ed4T, respectively. We investigated the relative contributions of these mutations, engineered into the strain NL4-3 background, to drug resistance, RT activity, and viral growth. Viral variants with single RT mutations (P119S or T165A) did not show resistance to 4'-Ed4T; however, M184V and P119S/T165A/M184V conferred three- and fivefold resistance, respectively, compared with that of the wild-type virus. The P119S/M184V and T165A/M184V variants showed about fourfold resistance to 4'-Ed4T. The differences in the growth kinetics of the variants were not more than threefold. The purified RT of mutants with the P119S/M184V and T165A/M184V mutations were inhibited by 4'-Ed4TTP with 8- to 13-fold less efficiency than wild-type RT. M184V may be the primary resistance-associated mutation of 4'-Ed4T, and P119S and T165A are secondary mutations. On the basis of our findings and the results of structural modeling, a virus with a high degree of resistance to 4'-Ed4T (e.g., more than 50-fold resistance) will be difficult to develop. The previously observed 130-fold resistance of the virus with P119S/T165A/M184V to 4'-Ed4T may be partly due to mutations both in the RT sequence and outside the RT sequence.
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res 2009; 85:210-31. [PMID: 19616029 DOI: 10.1016/j.antiviral.2009.07.006] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Revised: 06/26/2009] [Accepted: 07/03/2009] [Indexed: 11/25/2022]
Abstract
Antiretroviral therapy has led to a significant decrease in human immunodeficiency virus (HIV)-related mortality. Approved antiretroviral drugs target different steps of the viral life cycle including viral entry (coreceptor antagonists and fusion inhibitors), reverse transcription (nucleoside and non-nucleoside inhibitors of the viral reverse transcriptase), integration (integrase inhibitors) and viral maturation (protease inhibitors). Despite the success of combination therapies, the emergence of drug resistance is still a major factor contributing to therapy failure. Viral resistance is caused by mutations in the HIV genome coding for structural changes in the target proteins that can affect the binding or activity of the antiretroviral drugs. This review provides an overview of the molecular mechanisms involved in the acquisition of resistance to currently used and promising investigational drugs, emphasizing the structural role of drug resistance mutations. The optimization of current antiretroviral drug regimens and the development of new drugs are still challenging issues in HIV chemotherapy. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid), c/Nicolás Cabrera 1, Campus de Cantoblanco, 28049 Madrid, Spain.
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HIV-1 Can Persist in Aged Memory CD4+ T Lymphocytes With Minimal Signs of Evolution After 8.3 Years of Effective Highly Active Antiretroviral Therapy. J Acquir Immune Defic Syndr 2009; 50:345-53. [DOI: 10.1097/qai.0b013e318197eb04] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol 2008; 385:693-713. [PMID: 19022262 DOI: 10.1016/j.jmb.2008.10.071] [Citation(s) in RCA: 339] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 10/15/2008] [Accepted: 10/15/2008] [Indexed: 11/19/2022]
Abstract
The rapid replication of HIV-1 and the errors made during viral replication cause the virus to evolve rapidly in patients, making the problems of vaccine development and drug therapy particularly challenging. In the absence of an effective vaccine, drugs are the only useful treatment. Anti-HIV drugs work; so far drug therapy has saved more than three million years of life. Unfortunately, HIV-1 develops resistance to all of the available drugs. Although a number of useful anti-HIV drugs have been approved for use in patients, the problems associated with drug toxicity and the development of resistance means that the search for new drugs is an ongoing process. The three viral enzymes, reverse transcriptase (RT), integrase (IN), and protease (PR) are all good drug targets. Two distinct types of RT inhibitors, both of which block the polymerase activity of RT, have been approved to treat HIV-1 infections, nucleoside analogs (NRTIs) and nonnucleosides (NNRTIs), and there are promising leads for compounds that either block the RNase H activity or block the polymerase in other ways. A better understanding of the structure and function(s) of RT and of the mechanism(s) of inhibition can be used to generate better drugs; in particular, drugs that are effective against the current drug-resistant strains of HIV-1.
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Affiliation(s)
- Stefan G Sarafianos
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO 65211, USA
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Li N, Wang Y, Pothukuchy A, Syrett A, Husain N, Gopalakrisha S, Kosaraju P, Ellington AD. Aptamers that recognize drug-resistant HIV-1 reverse transcriptase. Nucleic Acids Res 2008; 36:6739-51. [PMID: 18948292 PMCID: PMC2588506 DOI: 10.1093/nar/gkn775] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Drug-resistant variants of HIV-1 reverse transcriptase (RT) are also known to be resistant to anti-RT RNA aptamers. In order to be able to develop diagnostics and therapies that can focus on otherwise drug-resistant viruses, we have isolated two aptamers against a well-known, drug-resistant HIV-1 RT, Mutant 3 (M3) from the multidrug-resistant HIV-1 RT panel. One aptamer, M302, bound M3 but showed no significant affinity for wild-type (WT) HIV-1 RT, while another aptamer, 12.01, bound to both M3 and WT HIV-1 RTs. In contrast to all previously selected anti-RT aptamers, neither of these aptamers showed observable inhibition of either polymerase or RNase H activities. Aptamers M302 and 12.01 competed with one another for binding to M3, but they did not compete with a pseudoknot aptamer for binding to the template/primer cleft of WT HIV-1 RT. These results represent the surprising identification of an additional RNA-binding epitope on the surface of HIV-1 RT. M3 and WT HIV-1 RTs could be distinguished using an aptamer-based microarray. By probing protein conformation as a correlate to drug resistance we introduce an additional and useful measure for determining HIV-1 drug resistance.
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Affiliation(s)
- Na Li
- Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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Bisphosphonate inhibitors of ATP-mediated HIV-1 reverse transcriptase catalyzed excision of chain-terminating 3'-azido, 3'-deoxythymidine: a QSAR investigation. Bioorg Med Chem 2008; 16:8959-67. [PMID: 18789701 DOI: 10.1016/j.bmc.2008.08.047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 08/11/2008] [Accepted: 08/22/2008] [Indexed: 11/20/2022]
Abstract
We report the results of an investigation of the inhibition of the ATP-mediated HIV-1 reverse transcriptase catalyzed phosphorolysis in vitro of AZT from AZT-terminated DNA primers by a series of 42 bisphosphonates. The four most active compounds possess neutral, halogen-substituted phenyl or biphenyl sidechains and have IC(50) values < 1 microM in excision inhibition assays. Use of two comparative molecular similarity analysis methods to analyze these inhibition results yielded a classification model with an overall accuracy of 94%, and a regression model having good accord with experiment (q(2)=0.63, r(2)=0.91), with the experimental activities being predicted within, on average, a factor of 2. The most active species had little or no toxicity against three human cell lines (IC(50)(avg) > 200 microM). These results are of general interest since they suggest that it may be possible to develop potent bisphosphonate-based AZT-excision inhibitors with little cellular toxicity, opening up a new route to restoring AZT sensitivity in otherwise resistant HIV-1 strains.
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Abstract
OBJECTIVE To develop an improved model for the genetic basis of reduced susceptibility to tenofovir in vitro. METHODS A dataset of 532 HIV-1 subtype B reverse transcriptase genotypes for which matched phenotypic susceptibility data were available was assembled, both as a continuous (transformed) dataset and a categorical dataset generated by imposing a cut-off on the basis of earlier studies of in-vivo response of 1.4-fold. Models were generated using stepwise regression, decision tree and random forest approaches on both the continuous and categorical data. Models were compared by mean squared error (continuous models), or by misclassification rates by nested crossvalidation. RESULTS From the continuous dataset, stepwise linear regression, regression tree and regression forest methods yielded models with MSE of 0.46, 0.48 and 0.42 respectively. Amino acids 215, 65, 41, 67, 184 and 151 in HIV-1 reverse transcriptase were identified in all three models and amino acid 210 in two. The categorical data yielded logistic regression, classification tree and forest models with misclassification rates of 26, 24 and 23%, respectively. Amino acids 215, 65 and 67 appeared in all; 41, 184, 210 and 151 were also included in the classification forest model. CONCLUSION The random forests approach has yielded a substantial improvement in the available models to describe the genetic basis of reduced susceptibility to tenofovir in vitro. The most important sites in these models are amino acid sites 215, 65, 41, 67, 184, 151 and 210 in HIV-1 reverse transcriptase.
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HIV-1 reverse transcriptase inhibitor resistance mutations and fitness: a view from the clinic and ex vivo. Virus Res 2008; 134:104-23. [PMID: 18289713 DOI: 10.1016/j.virusres.2007.12.021] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 12/27/2007] [Accepted: 12/28/2007] [Indexed: 01/04/2023]
Abstract
Genetic diversity plays a key role in human immunodeficiency virus (HIV) adaptation, providing a mechanism to escape host immune responses and develop resistance to antiretroviral drugs. This process is driven by the high-mutation rate during DNA synthesis by reverse transcriptase (RT), by the large viral populations, by rapid viral turnover, and by the high-recombination rate. Drugs targeting HIV RT are included in all regimens of highly active antiretroviral therapy (HAART), which helps to reduce the morbidity and mortality of HIV-infected patients. However, the emergence of resistant viruses is a significant obstacle to effective long-term management of HIV infection and AIDS. The increasing complexity of antiretroviral regimens has favored selection of HIV variants harboring multiple drug resistance mutations. Evolution of drug resistance is characterized by severe fitness losses when the drug is not present, which can be partially overcome by compensatory mutations or other adaptive changes that restore replication capacity. Here, we review the impact of mutations conferring resistance to nucleoside and nonnucleoside RT inhibitors on in vitro and in vivo fitness, their involvement in pathogenesis, persistence upon withdrawal of treatment, and transmission. We describe the techniques used to estimate viral fitness, the molecular mechanisms that help to improve the viral fitness of drug-resistant variants, and the clinical implications of viral fitness data, by exploring the potential relationship between plasma viral load, drug resistance, and disease progression.
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Martinez-Cajas JL, Wainberg MA. Antiretroviral therapy : optimal sequencing of therapy to avoid resistance. Drugs 2008; 68:43-72. [PMID: 18081372 DOI: 10.2165/00003495-200868010-00004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the second decade of highly active antiretroviral therapy, drug regimens offer more potent, less toxic and more durable choices. However, strategies addressing convenient sequential use of active antiretroviral combinations are rarely presented in the literature. Studies have seldom directly addressed this issue, despite it being a matter of daily use in clinical practice. This is, in part, because of the complexity of HIV-1 resistance information as well as the complexity of designing these types of studies. Nevertheless, several principles can effectively assist the planning of antiretroviral drug sequencing. The introduction of tenofovir disoproxil fumarate, abacavir and emtricitabine into current nucleoside backbone options, with each of them selecting for an individual pattern of resistance mutations, now permits sequencing in the context of previously popular thymidine analogues (zidovudine and stavudine). Similarly, newer ritonavir-boosted protease inhibitors could potentially be sequenced in a manner that uses the least cross-resistance prone protease inhibitor at the start of therapy, while leaving the most cross-resistance prone drugs for later, as long as there is rationale to employ such a compound because of its utility against commonly observed drug-resistant forms of HIV-1.
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Affiliation(s)
- Jorge L Martinez-Cajas
- McGill University AIDS Center, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
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Huigen MCDG, van Ham PM, de Graaf L, Kagan RM, Boucher CAB, Nijhuis M. Identification of a novel resistance (E40F) and compensatory (K43E) substitution in HIV-1 reverse transcriptase. Retrovirology 2008; 5:20. [PMID: 18271957 PMCID: PMC2276231 DOI: 10.1186/1742-4690-5-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 02/13/2008] [Indexed: 01/05/2023] Open
Abstract
Background HIV-1 nucleoside reverse transcriptase inhibitors (NRTIs) have been used in the clinic for over twenty years. Interestingly, the complete resistance pattern to this class has not been fully elucidated. Novel mutations in RT appearing during treatment failure are still being identified. To unravel the role of two of these newly identified changes, E40F and K43E, we investigated their effect on viral drug susceptibility and replicative capacity. Results A large database (Quest Diagnostics database) was analysed to determine the associations of the E40F and K43E changes with known resistance mutations. Both amino acid changes are strongly associated with the well known NRTI-resistance mutations M41L, L210W and T215Y. In addition, a strong positive association between these changes themselves was observed. A panel of recombinant viruses was generated by site-directed mutagenesis and phenotypically analysed. To determine the effect on replication capacity, competition and in vitro evolution experiments were performed. Introduction of E40F results in an increase in Zidovudine resistance ranging from nine to fourteen fold depending on the RT background and at the same time confers a decrease in viral replication capacity. The K43E change does not decrease the susceptibility to Zidovudine but increases viral replication capacity, when combined with E40F, demonstrating a compensatory role for this codon change. Conclusion In conclusion, we have identified a novel resistance (E40F) and compensatory (K43E) change in HIV-1 RT. Further research is indicated to analyse the clinical importance of these changes.
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Affiliation(s)
- Marleen C D G Huigen
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands.
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Quiñones-Mateu ME, Moore-Dudley DM, Jegede O, Weber J, J Arts E. Viral drug resistance and fitness. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2008; 56:257-96. [PMID: 18086415 DOI: 10.1016/s1054-3589(07)56009-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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