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Reddy N, Papathanasopoulos M, Steegen K, Basson AE. K103N, V106M and Y188L Significantly Reduce HIV-1 Subtype C Phenotypic Susceptibility to Doravirine. Viruses 2024; 16:1493. [PMID: 39339969 PMCID: PMC11437401 DOI: 10.3390/v16091493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 09/13/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
Doravirine (DOR) is a non-nucleoside reverse transcriptase inhibitor (NNRTI) with efficacy against some NNRTI-resistant mutants. Although DOR resistance mutations are established for HIV-1 subtype B, it is less clear for non-B subtypes. This study investigated prevalent NNRTI resistance mutations on DOR susceptibility in HIV-1 subtype C. Prevalent drug resistance mutations were identified from a South African genotypic drug resistance testing database. Mutations, single or in combination, were introduced into replication-defective pseudoviruses and assessed for DOR susceptibility in vitro. The single V106M and Y188L mutations caused high-level resistance while others did not significantly impact DOR susceptibility. We observed an agreement between our in vitro and the Stanford HIVdb predicted susceptibilities. However, the F227L mutation was predicted to cause high-level DOR resistance but was susceptible in vitro. Combinations of mutations containing K103N, V106M or Y188L caused high-level resistance, in agreement with the predictions. These mutations are frequently observed in patients failing efavirenz- or nevirapine-based first-line regimens. However, they are also observed in those failing a protease inhibitor-based second-line regimen, as we have observed in our database. Genotypic drug resistance testing is therefore vital prior to the initiation of DOR-based treatment for those previously exposed to efavirenz or nevirapine.
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Affiliation(s)
- Nikita Reddy
- HIV Pathogenesis Research Unit, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Maria Papathanasopoulos
- HIV Pathogenesis Research Unit, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Kim Steegen
- Department of Molecular Medicine and Haematology, School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Adriaan Erasmus Basson
- HIV Pathogenesis Research Unit, University of the Witwatersrand, Johannesburg 2193, South Africa
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Boyce CL, Sils T, Milne RS, Wallner JJ, Hardy SR, Ko D, Wong-On-Wing A, Mackey M, Higa N, Beck IA, Styrchak SM, DeMarrais P, Tierney C, Fowler MG, Frenkel LM. Impact of Human Immunodeficiency Virus Drug Resistance Mutations Detected in Women Prior to Antiretroviral Therapy With Efavirenz + Tenofovir Disoproxil Fumarate + Lamivudine (or Emtricitabine). Open Forum Infect Dis 2024; 11:ofae383. [PMID: 39050228 PMCID: PMC11267229 DOI: 10.1093/ofid/ofae383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024] Open
Abstract
Background Two large studies suggest that resistance mutations to only nonnucleoside reverse transcriptase inhibitors (NNRTI) did not increase the risk of virologic failure during antiretroviral therapy (ART) with efavirenz/tenofovir disoproxil fumarate/lamivudine (or emtricitabine). We retrospectively evaluated a third cohort to determine the impact of NNRTI resistance on the efficacy of efavirenz-based ART. Methods Postpartum women living with human immunodeficiency virus (HIV) were studied if they initiated efavirenz-based ART because of the World Health Organization's recommendation for universal ART. Resistance was detected by Sanger genotyping plasma prior to efavirenz-based ART and at virologic failure (HIV RNA >400 copies/mL). Logistic regression examined relationships between pre-efavirenz genotypes and virologic failure. Results Pre-efavirenz resistance was detected in 169 of 1223 (13.8%) participants. By month 12 of efavirenz-based ART, 189 of 1233 (15.3%) participants had virologic failure. Rates of virologic failure did not differ by pre-efavirenz NNRTI resistance. However, while pre-efavirenz nucleos(t)ide reverse transcriptase inhibitors (NRTI) and NNRTI resistance was rare (8/1223 [0.7%]) this genotype increased the odds (adjusted odds ratio, 11.2 [95% confidence interval, 2.21-72.2]) of virologic failure during efavirenz-based ART. Age, time interval between last viremic visit and efavirenz initiation, clinical site, viremia at delivery, hepatitis B virus coinfection, and antepartum regimen were also associated with virologic failure. Conclusions Resistance to NNRTI alone was prevalent and dual-class (NRTI and NNRTI) resistance was rare in this cohort, with only the latter associated with virologic failure. This confirms others' findings that, if needed, efavirenz-based ART offers most people an effective alternative to dolutegravir-based ART.
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Affiliation(s)
- Ceejay L Boyce
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tatiana Sils
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ross S Milne
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Jackson J Wallner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Samantha R Hardy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Daisy Ko
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Annie Wong-On-Wing
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Malia Mackey
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nikki Higa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid A Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sheila M Styrchak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Patricia DeMarrais
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Camlin Tierney
- Center for Biostatistics in AIDS Research, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mary G Fowler
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lisa M Frenkel
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
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Jennings L, Kellermann T, Spinelli M, Nkantsu Z, Cogill D, van Schalkwyk M, Decloedt E, van Zyl G, Orrell C, Gandhi M. Drug Resistance, Rather than Low Tenofovir Levels in Blood or Urine, Is Associated with Tenofovir, Emtricitabine, and Efavirenz Failure in Resource-Limited Settings. AIDS Res Hum Retroviruses 2022; 38:455-462. [PMID: 34779228 PMCID: PMC9225825 DOI: 10.1089/aid.2021.0135] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The high cost of viral load (VL) testing limits its use for antiretroviral therapy (ART) adherence support. A low-cost lateral flow urine tenofovir (TFV) rapid assay predicts pre-exposure prophylaxis breakthroughs, but has not yet been investigated in HIV treatment. We therefore evaluated its utility in a pilot cross-sectional study of TFV-containing ART recipients at an increased risk of virologic failure (VF). Participants who had a treatment interruption ≥30 days or had ≥1 episode of viremia (VL ≥400 copies/mL) in the previous year were recruited from a public health setting in Cape Town, South Africa. Self-reported adherence data were collected, the urine TFV assay performed, and concurrent TFV-diphosphate analyzed in dried blood spots. VL testing was done concurrently and, if viremic, genotypic HIV drug resistance testing was performed. Of 48 participants, 18 (37.5%) had VL (>400 copies/mL) at the time of the study, including 16 of 39 receiving efavirenz (EFV), 2 of 6 receiving protease inhibitors, and 0 of 3 receiving dolutegravir. Resistance testing succeeded in 17/18, of which 14 had significant mutations compromising ≥2 agents of the current EFV-based regimen. Of these 14, all had detected urine TFV. Urine TFV was undetectable in two out of three without regimen-relevant resistance; p = .02. In participants on EFV-based regimens returning to care, VF was largely due to viral resistance, where detectable urine TFV had 100% sensitivity (14/14 participants) in predicting resistance. Conversely, when undetectable, the urine-based assay could be used to preclude participants with poor adherence from undergoing costly HIV drug resistance testing.
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Affiliation(s)
- Lauren Jennings
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Tracy Kellermann
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Matthew Spinelli
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, California, USA
| | - Zukiswa Nkantsu
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Dolphina Cogill
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Marije van Schalkwyk
- Division of Infectious Diseases, Department of Medicine, Stellenbosch University, Cape Town, South Africa
| | - Eric Decloedt
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Stellenbosch University, Faculty of Medicine and Health Sciences, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Catherine Orrell
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, South Africa
| | - Monica Gandhi
- Division of HIV, Infectious Diseases, and Global Medicine at UCSF/San Francisco General Hospital, San Francisco, California, USA
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Henerico S, Mikasi SG, Kalluvya SE, Brauner JM, Abdul S, Lyimo E, Desderius B, Korn K, van Zyl G, Jacobs GB, Preiser W, Kasang C. Prevalence and patterns of HIV drug resistance in patients with suspected virological failure in North-Western Tanzania. J Antimicrob Chemother 2022; 77:483-491. [PMID: 35107140 PMCID: PMC8809186 DOI: 10.1093/jac/dkab406] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND More than 15 million people in sub-Saharan Africa receive ART. Treatment failure is common, but the role of HIV drug resistance in treatment failure is largely unknown because drug resistance testing is not routinely done. This study determined the prevalence and patterns of HIV drug resistance in patients with suspected virological failure. MATERIALS AND METHODS A single high viral load of >1000 viral RNA copies/mL of plasma at any point during ART was considered as suspected virological failure. HIV-1 RNA was extracted from plasma samples of these patients using the QIAamp Viral RNA kit. The protease and part of the RT regions of the HIV pol gene were characterized. RESULTS Viral load was determined in 317 patients; 64 (20.2%) had suspected virological failure. We successfully genotyped 56 samples; 48 (85.7%) had at least one major resistance-associated mutation (RAM). Common mutations in RT were M184V (75%), T215Y (41.1%), K103N (39.3%), M41L (32.1%), D67DN (30.3%), G190A (28.6%) and A98G (26.8%). No RAMs were detected in ART regimens based on a ritonavir-boosted PI. CONCLUSIONS The Tanzanian national guidelines define 'virological failure' as two consecutive viral load measurement results, at 3 month intervals, above the WHO threshold (1000 copies/mL). Here, we show that a single viral load above the WHO threshold is associated with high rates of RAMs. This suggests that a single high viral load measurement could be used to predict virological failure and avoid delays in switching patients from first-line to higher genetic barrier second-line regimens.
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Affiliation(s)
- Shimba Henerico
- Bugando Medical Centre, Mwanza, United Republic of Tanzania.,Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Sello Given Mikasi
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Samuel Elias Kalluvya
- Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Jan M Brauner
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Seif Abdul
- Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Eric Lyimo
- National Institute of Medical Research, Mwanza, United Republic of Tanzania
| | - Bernard Desderius
- Bugando Medical Centre, Mwanza, United Republic of Tanzania.,Catholic University of Health and Allied Sciences, Bugando Medical Centre, Mwanza, United Republic of Tanzania
| | - Klaus Korn
- Institute of Clinical and Molecular Virology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University/National Health Laboratory Service (NHLS) Tygerberg, South Africa
| | - Christa Kasang
- German Leprosy and Tuberculosis Relief Association, Wuerzburg, Germany.,Medical Mission Institute, Wuerzburg, Germany
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Nyandiko W, Holland S, Vreeman R, DeLong AK, Manne A, Novitsky V, Ngeresa A, Chory A, Aluoch J, Orido M, Jepkemboi E, Sam SS, Caliendo AM, Ayaya S, Hogan JW, Kantor R. HIV-1 Treatment Failure, Drug Resistance, and Clinical Outcomes in Perinatally Infected Children and Adolescents Failing First-Line Antiretroviral Therapy in Western Kenya. J Acquir Immune Defic Syndr 2022; 89:231-239. [PMID: 34723922 PMCID: PMC8752470 DOI: 10.1097/qai.0000000000002850] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 10/19/2021] [Indexed: 02/03/2023]
Abstract
BACKGROUND Long-term impact of drug resistance in perinatally infected children and adolescents living with HIV (CALWH) is poorly understood. We determined drug resistance and examined its long-term impact on failure and mortality in Kenyan CALWH failing first-line non-nucleoside reverse transcriptase inhibitor-based antiretroviral therapy (ART). SETTING Academic Model Providing Access to Healthcare, western Kenya. METHODS Participants were enrolled in 2010-2013 (timepoint 1) and a subsample re-enrolled after 4-7 years (timepoint 2). Viral load (VL) was performed on timepoint 1 samples, with genotyping of those with detectable VL. Primary endpoints were treatment failure (VL >1000 copies/mL) at and death before timepoint 2. Multinomial regression analysis was used to characterize resistance effect on death, failure, and loss-to-follow-up, adjusting for key variables. RESULTS The initial cohort (n = 480) was 52% (n = 251) female, median age 8 years, median CD4% 31%, 79% (n = 379) on zidovudine/abacavir + lamivudine + efavirenz/nevirapine for median 2 years. Of these, 31% (n = 149) failed at timepoint 1. Genotypes at timepoint 1, available on n = 128, demonstrated 93% (n = 119) extensive resistance, affecting second line. Of 128, 22 failed at timepoint 2, 17 died, and 32 were lost to follow-up before timepoint 2. Having >5 resistance mutations at timepoint 1 was associated with higher mortality [relative risk ratio (RRR) = 8.7, confidence interval (CI) 2.1 to 36.3] and loss to follow-up (RRR = 3.2, CI 1.1 to 9.2). Switching to second line was associated with lower mortality (RRR <0.05, CI <0.05 to 0.1) and loss to follow-up (RRR = 0.1, CI <0.05 to 0.3). CONCLUSION Extensive resistance and limited switch to second line in perinatally infected Kenyan CALWH failing first-line ART were associated with long-term failure and mortality. Findings emphasize urgency for interventions to sustain effective, life-long ART in this vulnerable population.
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Affiliation(s)
- Winstone Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Rachel Vreeman
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | | | - Anthony Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Ashley Chory
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Josephine Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Millicent Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Eslyne Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | | | | | - Samuel Ayaya
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University College of Health Sciences, Eldoret, Kenya
| | - Joseph W Hogan
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Brown University, Providence, RI, USA
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