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Minimal Cross-resistance to Tenofovir in Children and Adolescents Failing ART Makes Them Eligible for Tenofovir-Lamivudine-Dolutegravir Treatment. Pediatr Infect Dis J 2022; 41:827-834. [PMID: 35895893 PMCID: PMC9508940 DOI: 10.1097/inf.0000000000003647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Fixed-dose combination of dolutegravir (DTG) with tenofovir disoproxil fumarate (TDF) and lamivudine (3TC) likely improves adherence and has a favorable resistance profile. We evaluated predicted efficacy of TLD (TDF-3TC-DTG) in children and adolescents failing abacavir (ABC), zidovudine (AZT), or TDF containing regimens. METHODS Drug resistance mutations were analyzed in a retrospective dataset of individuals <19 years of age, failing ABC (n = 293) AZT (n = 288) or TDF (n = 69) based treatment. Pol sequences were submitted to Stanford HIVdb v8.9. Genotypic susceptibility scores were calculated for various DTG-containing regimens. RESULTS Genotypes were assessed for 650 individuals with a median age of 14 years (IQR 10-17 years). More individuals failed a protease inhibitor (PI)-based (78.3%) than a non-nucleoside reverse transcriptase inhibitors (NNRTI)-based (21.7%) regimen. Most individuals in the AZT group (n = 288; 94.4%) failed a PI-based regimen, compared with 71.0% and 64.2% in the TDF (n = 69) and ABC group (n = 293). Genotypic sensitivity scores <2 to TLD were observed in 8.5% and 9.4% of ABC- and AZT-exposed individuals, compared with 23.2% in the TDF group. The M184V mutation was most often detected in the ABC group (70.6%) versus 60.0% and 52.4% in TDF and AZT groups. The presence of K65R was rare (n = 13, 2.0%) and reduced TLD susceptibility was commonly caused by accumulation of nucleoside reverse transcriptase inhibitor (NRTI) mutations. CONCLUSIONS Cross-resistance to TDF was limited, further reducing concerns about use of transition to TLD in children and adolescents. The NADIA trial has subsequently shown that patients failing a TDF/3TC/EFV regimen can safely be transitioned to a TLD regimen but we do not have data for patients failing an ABC/3TC/NNRTI or PI regimens. Frequent virological monitoring is recommended after switch to DTG, especially in children continuing ABC in the backbone. Clinical studies correlating predicted resistance with clinical outcomes, especially in settings without access to genotyping, are required.
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Nationwide Study of Drug Resistance Mutations in HIV-1 Infected Individuals under Antiretroviral Therapy in Brazil. Int J Mol Sci 2021; 22:ijms22105304. [PMID: 34069929 PMCID: PMC8157590 DOI: 10.3390/ijms22105304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/02/2022] Open
Abstract
The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p < 0.001). Among the two most prevalent HIV-1 subtypes (B and C) there was a significant (p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.
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Kladwang W, Topkar VV, Liu B, Rangan R, Hodges TL, Keane SC, Al-Hashimi H, Das R. Anomalous Reverse Transcription through Chemical Modifications in Polyadenosine Stretches. Biochemistry 2020; 59:2154-2170. [PMID: 32407625 DOI: 10.1021/acs.biochem.0c00020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Thermostable reverse transcriptases are workhorse enzymes underlying nearly all modern techniques for RNA structure mapping and for the transcriptome-wide discovery of RNA chemical modifications. Despite their wide use, these enzymes' behaviors at chemical modified nucleotides remain poorly understood. Wellington-Oguri et al. recently reported an apparent loss of chemical modification within putatively unstructured polyadenosine stretches modified by dimethyl sulfate or 2' hydroxyl acylation, as probed by reverse transcription. Here, reanalysis of these and other publicly available data, capillary electrophoresis experiments on chemically modified RNAs, and nuclear magnetic resonance spectroscopy on (A)12 and variants show that this effect is unlikely to arise from an unusual structure of polyadenosine. Instead, tests of different reverse transcriptases on chemically modified RNAs and molecules synthesized with single 1-methyladenosines implicate a previously uncharacterized reverse transcriptase behavior: near-quantitative bypass through chemical modifications within polyadenosine stretches. All tested natural and engineered reverse transcriptases (MMLV; SuperScript II, III, and IV; TGIRT-III; and MarathonRT) exhibit this anomalous bypass behavior. Accurate DMS-guided structure modeling of the polyadenylated HIV-1 3' untranslated region requires taking into account this anomaly. Our results suggest that poly(rA-dT) hybrid duplexes can trigger an unexpectedly effective reverse transcriptase bypass and that chemical modifications in mRNA poly(A) tails may be generally undercounted.
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Affiliation(s)
- Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Ved V Topkar
- Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, California 94305, United States
| | - Tracy L Hodges
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States.,Department of Chemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States.,Biophysics Program, Stanford University, Stanford, California 94305, United States.,Department of Physics, Stanford University, Stanford, California 94305, United States
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4
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Telele NF, Kalu AW, Gebre-Selassie S, Fekade D, Marrone G, Grossmann S, Neogi U, Tegbaru B, Sönnerborg A. A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort. BMC Infect Dis 2019; 19:569. [PMID: 31262272 PMCID: PMC6604127 DOI: 10.1186/s12879-019-4196-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 06/17/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) was rolled-out in Ethiopia in 2005, but there are no reports on outcome of ART and human immunodeficiency virus drug resistance (HIVDR) at national level. We described acquired drug resistance mutations in pol gene and performed a viral genome wide association study in virologic treatment failure patients who started first line ART during 2009-2011 in the first large countrywide HIV cohort in Ethiopia. METHODS The outcome of tenofovir (TDF)- and zidovudine (ZDV)-based ART was defined in 874 ART naïve patients using the on-treatment (OT) and intention-to-treat (ITT) analyses. Genotypic resistance testing was done in patients failing ART (> 1000 copies/ml) at month 6 and 12. Near full-length genome sequencing (NFLG) was used to assess amino acid changes in HIV-1 gag, pol, vif, vpr, tat, vpu, and nef genes between paired baseline and month 6 samples. RESULTS High failure rates were found in ITT analysis at month 6 and 12 (23.3%; 33.9% respectively). Major nucleoside and non-nucleoside reverse transcriptase (NRTI/NNRTI) drug resistance mutations were detected in most failure patients at month 6 (36/47; 77%) and month 12 (20/30; 67%). A high rate of K65R was identified only in TDF treated patients (35.7%; 50.0%, respectively). No significant difference was found in failure rate or extent of HIVDR between TDF- and ZDV- treated patients. All target regions of interest for HIVDR were described by NFLG in 16 patients tested before initiation of ART and at month 6. CONCLUSION In this first Ethiopian national cohort, a high degree of HIVDR was seen among ART failure patients, independent on whether TDF- or ZDV was given. However, the major reason to ART failure was lost-to-follow-up rather than virologic failure. Our NFLG assay covered all relevant target genes for antiretrovirals and is an attractive alternative for HIVDR surveillance.
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Affiliation(s)
- Nigus Fikrie Telele
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Amare Worku Kalu
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Solomon Gebre-Selassie
- Department of Microbiology, Immunology and Parasitology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Fekade
- Department of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gaetano Marrone
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sebastian Grossmann
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Wellcome Trust Sanger Institute, Cancer, Ageing and Somatic Mutation Programme, Cambridge, UK
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
| | - Belete Tegbaru
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Alfred Nobels Allé 8, 141 83 Huddinge, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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HIV-1 Subtype C with PYxE Insertion Has Enhanced Binding of Gag-p6 to Host Cell Protein ALIX and Increased Replication Fitness. J Virol 2019; 93:JVI.00077-19. [PMID: 30760577 DOI: 10.1128/jvi.00077-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/07/2019] [Indexed: 02/02/2023] Open
Abstract
Human immunodeficiency virus type 1 subtype C (HIV-1C) has a natural deletion of a YPxL motif in its Gag-p6 late domain. This domain mediates the binding of Gag to host cell protein ALIX and subsequently facilitates viral budding. In a subset of HIV-1C-infected individuals, the tetrapeptide insertion PYxE has been identified at the deleted YPxL motif site. Here, we report the consequences of PYxE insertion on the interaction with ALIX and the relevance regarding replication fitness and drug sensitivity. In our three HIV-1C cohorts, PYKE and PYQE were most prevalent among PYxE variants. Through in silico predictions and in vitro experiments, we showed that HIV-1C Gag has an increased binding to ALIX when the PYxE motif is present. To go more into the clinical relevance of the PYxE insertion, we obtained patient-derived gag-pol sequences from HIV-1CPYxEi viruses and inserted them in a reference HIV-1 sequence. Viral growth was increased, and the sensitivity to the protease inhibitor (PI) lopinavir (LPV) and nucleoside reverse transcriptase inhibitor tenofovir alafenamide (TAF) was decreased for some of the HIV-1C PYxE variants compared to that of wild-type variants. Our data suggest that PYxE insertion in Gag restores the ability of Gag to bind ALIX and correlates with enhanced viral fitness in the absence or presence of LPV and TAF. The high prevalence and increased replication fitness of the HIV-1C virus with PYxE insertion indicates the clinical importance of these viral variants.IMPORTANCE Genomic differences within HIV-1 subtypes is associated with various degrees of viral spread, disease progression, and clinical outcome. Viral budding is essential in the HIV-1 life cycle and mainly mediated through the interaction of Gag with host proteins. Two motifs within Gag-p6 mediate binding of host cell proteins and facilitate budding. HIV-1C has a natural deletion of one of these two motifs, resulting in an inability to bind to host cell protein ALIX. Previously, we have identified a tetrapeptide (PYxE) insertion at this deleted motif site in a subset of HIV-1C patients. Here, we report the incidence of PYxE insertions in three different HIV-1C cohorts, and the insertion restores the binding of Gag to ALIX. It also increases viral growth even in the presence of the antiretroviral drugs lopinavir and tenofovir alafenamide. Hence, PYxE insertion in HIV-1C might be biologically relevant for viruses and clinically significant among patients.
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Derache A, Iwuji CC, Danaviah S, Giandhari J, Marcelin AG, Calvez V, de Oliveira T, Dabis F, Pillay D, Gupta RK. Predicted antiviral activity of tenofovir versus abacavir in combination with a cytosine analogue and the integrase inhibitor dolutegravir in HIV-1-infected South African patients initiating or failing first-line ART. J Antimicrob Chemother 2019; 74:473-479. [PMID: 30380053 PMCID: PMC6337894 DOI: 10.1093/jac/dky428] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/13/2018] [Accepted: 09/18/2018] [Indexed: 02/07/2023] Open
Abstract
Objectives The WHO recently recommended the use of a new first-line ART containing dolutegravir. We investigated the efficacy of NRTI backbones (tenofovir or abacavir with a cytosine analogue) in low- and middle-income countries where there is significant prior exposure to antiretrovirals and drug resistance to NRTIs. Methods Within the treatment-as-prevention study in South Africa, we selected participants with available next-generation sequencing (NGS) data for the HIV-1 pol gene at trial entry; they were either ART initiators (n = 1193) or already established on ART (n = 94). NGS of the HIV-1 pol gene was carried out using MiSeq technology; reverse transcriptase drug resistance mutations (DRMs) were detected at 5% (DRM5%) and 20% (DRM20%) for all 1287 participants. Genotypic susceptibility was assessed using the Stanford HIVDB resistance interpretation algorithm. Results NRTI DRM20% and DRM5% were detected among 5/1193 (0.4%) and 9/1193 (0.8%) of ART initiators, respectively. There was tenofovir exposure in 73/94 (77.7%) of those established on ART, with full susceptibility to abacavir in 57/94 (60.6%) and 56/94 (59.6%) for DRM20% and DRM5%, respectively, while 67/94 (71.3%) and 64/94 (68.1%) were fully susceptible to tenofovir, respectively. The differences between tenofovir and abacavir were not statistically significant at the 20% or 5% variant level (P = 0.16 and 0.29, respectively). NGS detection of variants at the 5% level increased detection of K65R in both naive and treated groups. One of 607 integrase sequences carried a DRM20% (Q148R). Conclusions Dolutegravir with a cytosine analogue plus tenofovir or abacavir appears to have similar efficacy in South Africans naive to ART. NGS should be considered in HIV drug resistance surveillance.
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Affiliation(s)
- Anne Derache
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Collins C Iwuji
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Institute for Global Health, University College London, London, UK
- Department of Global Health and Infection, Brighton and Sussex Medical School, Brighton, UK
| | - Siva Danaviah
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anne-Geneviève Marcelin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Vincent Calvez
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Laboratoire de virologie, F-75013 Paris, France
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - François Dabis
- Université de Bordeaux, ISPED, Centre INSERM 1219, Bordeaux, France
| | - Deenan Pillay
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Africa Health Research Institute (AHRI), KwaZulu-Natal, South Africa
- Division of Infection and Immunity, University College London, London, UK
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7
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Smit E, White E, Clark D, Churchill D, Zhang H, Collins S, Pillay D, Sabin C, Nelson M, Winston A, Jose S, Tostevin A, Dunn DT. An association between K65R and HIV-1 subtype C viruses in patients treated with multiple NRTIs. J Antimicrob Chemother 2018; 72:2075-2082. [PMID: 28379449 PMCID: PMC5890671 DOI: 10.1093/jac/dkx091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/28/2017] [Indexed: 11/13/2022] Open
Abstract
Objectives: HIV-1 subtype C might have a greater propensity to develop K65R mutations in patients with virological failure compared with other subtypes. However, the strong association between viral subtype and confounding factors such as exposure groups and ethnicity affects the calculation of this propensity. We exploited the diversity of viral subtypes within the UK to undertake a direct comparative analysis. Patients and methods: We analysed only sequences with major IAS-defined mutations from patients with virological failure. Prevalence of K65R was related to subtype and exposure to the NRTIs that primarily select for this mutation (tenofovir, abacavir, didanosine and stavudine). A multivariate logistic regression model quantified the effect of subtype on the prevalence of K65R, adjusting for previous and current exposure to all four specified drugs. Results: Subtype B patients (n = 3410) were mostly MSM (78%) and those with subtype C (n = 810) were mostly heterosexual (82%). K65R was detected in 7.8% of subtype B patients compared with 14.2% of subtype C patients. The subtype difference in K65R prevalence was observed irrespective of NRTI exposure and K65R was frequently selected by abacavir, didanosine and stavudine in patients with no previous exposure to tenofovir. Multivariate logistic regression confirmed that K65R was significantly more common in subtype C viruses (adjusted OR = 2.02, 95% CI = 1.55–2.62, P < 0.001). Conclusions: Patients with subtype C HIV-1 have approximately double the frequency of K65R in our database compared with other subtypes. The exact clinical implications of this finding need to be further elucidated.
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Affiliation(s)
- Erasmus Smit
- Public Health Laboratory Birmingham, Public Health England, Heartlands Hospital, Birmingham, UK
| | - Ellen White
- MRC CTU at UCL, University College London, London, UK
| | | | - Duncan Churchill
- Brighton and Sussex University Hospitals NHS Trust, Brighton, UK
| | - Hongyi Zhang
- Public Health Laboratory Cambridge, Public Health England, Addenbrooke's Hospital, Cambridge, UK
| | | | - Deenan Pillay
- Research Department of Infection, Division of Infection and Immunity, University College London, London, UK.,Wellcome Trust Africa Centre for Health and Population Sciences, University of KwaZulu Natal, Mtubatuba, South Africa
| | - Caroline Sabin
- Research Department of Infection and Population Health London, University College London, London, UK
| | - Mark Nelson
- Chelsea and Westminster Hospital, London, UK
| | - Alan Winston
- Section of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Sophie Jose
- Research Department of Infection and Population Health London, University College London, London, UK
| | - Anna Tostevin
- Research Department of Infection and Population Health London, University College London, London, UK
| | - David T Dunn
- Research Department of Infection and Population Health London, University College London, London, UK
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Increasing prevalence of K65K and K66K in HIV-1 subtype B reverse transcriptase. AIDS 2016; 30:2787-2793. [PMID: 27677159 DOI: 10.1097/qad.0000000000001272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Synonymous substitutions K65K/K66K in HIV-1 reverse transcriptase alleviate fitness and fidelity defects in HIV-1 molecular clones harboring thymidine analogue mutations (TAMs); however, their potential for transmission and persistence is unknown. Here, we investigated the temporal appearance of K65K/K66K relative to TAMs in a HIV-1 cohort, their prevalence over time, and their impact on viral fitness in the context of patient-derived reverse transcriptase sequences. METHODS Retrospective analyses of the temporal appearance and longitudinal prevalence of synonymous substitutions and drug resistance mutations were performed using the British Columbia Centre for Excellence in HIV/AIDS Drug Treatment Program (DTP) database. Plasma-derived HIV-1 from the DTP was used to generate infectious molecular clones. Growth competition assays were performed to determine viral fitness. RESULTS The prevalence of K65K/K66K in drug-naïve individuals tripled from 11% in 1997 to 37% in 2014 (P < 0.0001, n = 5221), with K66K mainly accounting for the increase. These mutations emerged in drug-treated individuals without TAMs in 14% of the cohort and conferred a fitness advantage in the context of patient-derived multidrug-resistant (MDR) virus in the absence of drug. CONCLUSION The appearance of K65K/K66K in drug-treated individuals was largely independent of TAMs, suggesting alternative factors are likely associated with their emergence. The increasing K65K/K66K prevalence to over a third of treatment-naïve individuals in the mostly subtype B DTP cohort and their ability to confer a fitness advantage to multidrug-resistant virus might explain the transmission and persistence of virus harbouring K65K/K66K in untreated individuals, and highlights their role in adaptive HIV-1 evolution.
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9
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Steegen K, Bronze M, Papathanasopoulos MA, van Zyl G, Goedhals D, Variava E, MacLeod W, Sanne I, Stevens WS, Carmona S. HIV-1 antiretroviral drug resistance patterns in patients failing NNRTI-based treatment: results from a national survey in South Africa. J Antimicrob Chemother 2016; 72:210-219. [PMID: 27659733 DOI: 10.1093/jac/dkw358] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Routine HIV-1 antiretroviral drug resistance testing for patients failing NNRTI-based regimens is not recommended in resource-limited settings. Therefore, surveys are required to monitor resistance profiles in patients failing ART. METHODS A cross-sectional survey was conducted amongst patients failing NNRTI-based regimens in the public sector throughout South Africa. Virological failure was defined as two consecutive HIV-1 viral load results >1000 RNA copies/mL. Pol sequences were obtained using RT-PCR and Sanger sequencing and submitted to Stanford HIVdb v7.0.1. RESULTS A total of 788 sequences were available for analysis. Most patients failed a tenofovir-based NRTI backbone (74.4%) in combination with efavirenz (82.1%) after median treatment duration of 36 months. K103N (48.9%) and V106M (34.9%) were the most common NNRTI mutations. Only one-third of patients retained full susceptibility to second-generation NNRTIs such as etravirine (36.5%) and rilpivirine (27.3%). After M184V/I (82.7%), K65R was the most common NRTI mutation (45.8%). The prevalence of K65R increased to 57.5% in patients failing a tenofovir regimen without prior stavudine exposure. Cross-resistance to NRTIs was often observed, but did not seem to affect the predicted activity of zidovudine as 82.9% of patients remained fully susceptible to this drug. CONCLUSIONS The introduction of tenofovir-based first-line regimens has dramatically increased the prevalence of K65R mutations in the HIV-1-infected South African population. However, most patients failing tenofovir-based regimens remained fully susceptible to zidovudine. Based on these data, there is currently no need to change either the recommended first- or second-line ART regimens in South Africa.
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Affiliation(s)
- K Steegen
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - M Bronze
- National Health Laboratory Service, Johannesburg, South Africa
| | - M A Papathanasopoulos
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - G van Zyl
- National Health Laboratory Service, Johannesburg, South Africa.,Division of Medical Virology, Stellenbosch University, Stellenbosch, South Africa
| | - D Goedhals
- National Health Laboratory Service, Johannesburg, South Africa.,Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein, South Africa
| | - E Variava
- Department of Internal Medicine, Klerksdorp Tshepong Hospital Complex, Klerksdorp, South Africa.,Department of Internal Medicine, University of the Witwatersrand, Johannesburg, South Africa.,Perinatal HIV Research Unit, Johannesburg, South Africa
| | - W MacLeod
- Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA.,Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - I Sanne
- Right to Care, Johannesburg, South Africa
| | - W S Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
| | - S Carmona
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.,National Health Laboratory Service, Johannesburg, South Africa
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10
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Manasa J, Danaviah S, Lessells R, Elshareef M, Tanser F, Wilkinson E, Pillay S, Mthiyane H, Mwambi H, Pillay D, de Oliveira T. Increasing HIV-1 Drug Resistance Between 2010 and 2012 in Adults Participating in Population-Based HIV Surveillance in Rural KwaZulu-Natal, South Africa. AIDS Res Hum Retroviruses 2016; 32:763-9. [PMID: 27002368 PMCID: PMC4971422 DOI: 10.1089/aid.2015.0225] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
As more human immunodeficiency virus (HIV)–infected patients access combination antiretroviral therapy (cART), higher proportions of newly infected patients may be infected with drug-resistant viruses. Regular surveillance of transmitted drug resistance (TDR) is required in southern Africa where high rates of transmission persist despite rapid expansion of ART. Dried blood spot samples from cART-naive participants from two rounds of an annual population-based HIV surveillance program in rural KwaZulu-Natal were tested for HIV RNA, and samples with HIV RNA >10,000 copies/ml were genotyped for drug resistance. The 2009 surveillance of drug resistance mutation (SDRM) list was used for drug resistance interpretation. The data were added to previously published data from the same program, and the χ2 test for trend was used to test for trend in estimated prevalence of any TDR. Seven hundred and one participants' data were analyzed: 67 (2010), 381 (2011), and 253 (2012). No TDR was detected in 2010. Years 2011 and 2012 had 18 participants with SDRMs 4.7% and 7.1%, respectively (p = .02, χ2 test for trend). The nonnucleoside reverse transcriptase inhibitor mutation, K103N, was the most common mutation, occurring in 27 (3.8%) of the participants, while nucleoside reverse transcriptase inhibitor (NRTI) SDRMs were detected in 10 (1.4%) of the participants, of whom eight had only a single NRTI SDRM. The increase in levels of drug resistance observed in this population could be a signal of increasing transmission of drug-resistant HIV. Thus, continued surveillance is critical to inform public health policies around HIV treatment and prevention.
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Affiliation(s)
- Justen Manasa
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California
| | - Siva Danaviah
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Richard Lessells
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Muna Elshareef
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, South Africa
| | - Frank Tanser
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Eduan Wilkinson
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Sureshnee Pillay
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Hloniphile Mthiyane
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Henry Mwambi
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, KwaZulu-Natal, South Africa
| | - Deenan Pillay
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
| | - Tulio de Oliveira
- Africa Centre for Population Health, University of KwaZulu-Natal, Mtubatuba, KwaZulu-Natal, South Africa
- Research Department of Infection, University College of London (UCL), London, United Kingdom
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Treatment failure and drug resistance in HIV-positive patients on tenofovir-based first-line antiretroviral therapy in western Kenya. J Int AIDS Soc 2016; 19:20798. [PMID: 27231099 PMCID: PMC4882399 DOI: 10.7448/ias.19.1.20798] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/31/2016] [Accepted: 04/26/2016] [Indexed: 12/03/2022] Open
Abstract
Introduction Tenofovir-based first-line antiretroviral therapy (ART) is recommended globally. To evaluate the impact of its incorporation into the World Health Organization (WHO) guidelines, we examined treatment failure and drug resistance among a cohort of patients on tenofovir-based first-line ART at the Academic Model Providing Access to Healthcare, a large HIV treatment programme in western Kenya. Methods We determined viral load (VL), drug resistance and their correlates in patients on ≥six months of tenofovir-based first-line ART. Based on enrolled patients’ characteristics, we described these measures in those with (prior ART group) and without (tenofovir-only group) prior non-tenofovir-based first-line ART using Wilcoxon rank sum and Fisher's exact tests. Results Among 333 participants (55% female; median age 41 years; median CD4 336 cells/µL), detectable (>40 copies/mL) VL was found in 18%, and VL>1000 copies/mL (WHO threshold) in 10%. Virologic failure at both thresholds was significantly higher in 217 participants in the tenofovir-only group compared with 116 in the prior ART group using both cut-offs (24% vs. 7% with VL>40 copies/mL; 15% vs. 1% with VL>1000 copies/mL). Failure in the tenofovir-only group was associated with lower CD4 values and advanced WHO stage. In 35 available genotypes from 51 participants in the tenofovir-only group with VL>40 copies/mL (69% subtype A), any resistance was found in 89% and dual-class resistance in 83%. Tenofovir signature mutation K65R occurred in 71% (17/24) of the patients infected with subtype A. Patients with K65R had significantly lower CD4 values, higher WHO stage and more resistance mutations. Conclusions In this Kenyan cohort, tenofovir-based first-line ART resulted in good (90%) virologic suppression including high suppression (99%) after switch from non-tenofovir-based ART. Lower virologic suppression (85%) and high observed resistance levels (89%) in the tenofovir-only group impact future treatment options, support recommendations for widespread VL monitoring in such resource limited settings to identify early treatment failure and suggest consideration of individualized resistance testing to design effective subsequent regimens.
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White E, Smit E, Churchill D, Collins S, Booth C, Tostevin A, Sabin C, Pillay D, Dunn DT. No Evidence That HIV-1 Subtype C Infection Compromises the Efficacy of Tenofovir-Containing Regimens: Cohort Study in the United Kingdom. J Infect Dis 2016; 214:1302-1308. [PMID: 27732929 PMCID: PMC5079361 DOI: 10.1093/infdis/jiw213] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 11/26/2022] Open
Abstract
Concern has been expressed that tenofovir-containing regimens may have reduced effectiveness in the treatment of human immunodeficiency virus type 1 (HIV-1) subtype C infections because of a propensity for these viruses to develop a key tenofovir-associated resistance mutation. We evaluated whether subtype influenced rates of virological failure in a cohort of 8746 patients from the United Kingdom who received a standard tenofovir-containing first-line regimen and were followed for a median of 3.3 years. In unadjusted analyses, the rate of failure was approximately 2-fold higher among patients infected with subtype C virus as compared to those with subtype B virus (hazard ratio [HR], 1.86; 95% confidence interval [CI], 1.50–2.31; P < .001). However, the increased risk was greatly attenuated in analyses adjusting for demographic and clinical factors (adjusted HR, 1.14; 95% CI, .83–1.58; P = .41). There were no differences between subtypes C and subtypes non-B and non-C in either univariate or multivariate analysis. These observations imply there is no intrinsic effect of viral subtype on the efficacy of tenofovir-containing regimens.
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Affiliation(s)
| | - Erasmus Smit
- Public Health England, Birmingham Heartlands Hospital
| | | | | | - Clare Booth
- Health Service Laboratories, Royal Free Hospital, London
| | | | | | - Deenan Pillay
- Division of Infection and Immunity, University College London.,Africa Centre for Population Health, University of KwaZulu-Natal, Durban, South Africa
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Skhosana L, Steegen K, Bronze M, Lukhwareni A, Letsoalo E, Papathanasopoulos MA, Carmona SC, Stevens WS. High prevalence of the K65R mutation in HIV-1 subtype C infected patients failing tenofovir-based first-line regimens in South Africa. PLoS One 2015; 10:e0118145. [PMID: 25659108 PMCID: PMC4320083 DOI: 10.1371/journal.pone.0118145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/05/2015] [Indexed: 12/04/2022] Open
Abstract
Background Tenofovir (TDF) has replaced stavudine (d4T) as the preferred nucleoside reverse transcriptase inhibitor (NRTI) in first-line regimens in South Africa, but limited information is available on the resistance patterns that develop after the introduction of TDF. This study investigated the antiretroviral drug resistance patterns in South African HIV-1 subtype C-infected patients failing stavudine- (d4T) and tenofovir- (TDF) based first-line regimens and assess the suitability of TDF as the preferred first-line nucleotide reverse transcriptase inhibitor (NRTI). Methods Resistance patterns of HIV-1 from 160 adult patients virologically failing TDF- (n = 80) and d4T- (n = 80) based first-line regimens were retrospectively analyzed. The pol gene was sequenced using an in-house protocol and mutations were analysed using the IAS-USA 2014 Drug Resistance Mutation list. Results Compared to d4T-exposed patients (n = 7), patients failing on a TDF-containing regimen (n = 43) were almost 5 times more likely to present with a K65R mutation (aRR 4.86 95% CI 2.29 – 10.34). Y115F was absent in the d4T group, and detected in 13.8% (n = 11) of TDF-exposed patients, p = 0.0007. Virus from 9 of the 11 patients (82.0%) who developed the Y115F mutation also developed K65R. Intermediate or high-level resistance to most NRTIs was common in the TDF-treatment group, but these patients twice more likely to remain susceptible to AZT as compared to those exposed to d4T (aRR 2.09 95% CI 1.13 – 3.90). Conclusion The frequency of the TDF induced K65R mutation was higher in our setting compared to non-subtype C dominated countries. However, despite the higher frequency of cross-resistance to NRTIs, most patients remained susceptible to AZT, which is reflected in the South African treatment guidelines that recommend AZT as an essential component of second-line regimens.
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Affiliation(s)
- Lindiwe Skhosana
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kim Steegen
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Michelle Bronze
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Azwidowi Lukhwareni
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Esrom Letsoalo
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Maria A. Papathanasopoulos
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sergio C. Carmona
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Wendy S. Stevens
- Department of Haematology and Molecular Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
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Emerging antiretroviral drug resistance in sub-Saharan Africa: novel affordable technologies are needed to provide resistance testing for individual and public health benefits. AIDS 2014; 28:2643-8. [PMID: 25493592 DOI: 10.1097/qad.0000000000000502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure. J Clin Virol 2014; 62:48-53. [PMID: 25542470 DOI: 10.1016/j.jcv.2014.11.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 11/08/2014] [Indexed: 11/21/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) allows the detection of minor variant HIV drug resistance mutations (DRMs). However data from new NGS platforms after Prevention-of-Mother-to-Child-Transmission (PMTCT) regimen failure are limited. OBJECTIVE To compare major and minor variant HIV DRMs with Illumina MiSeq and Life Technologies Ion Personal Genome Machine (PGM) in infants infected despite a PMTCT regimen. STUDY DESIGN We conducted a cross-sectional study of NGS for detecting DRMs in infants infected despite a zidovudine (AZT) and Nevirapine (NVP) regimen, before initiation of combination antiretroviral therapy. Sequencing was performed on PCR products from plasma samples on PGM and MiSeq platforms. Bioinformatic analyses were undertaken using a codon-aware version of the Smith-Waterman mapping algorithm and a mixture multinomial error filtering statistical model. RESULTS Of 15 infants, tested at a median age of 3.4 months after birth, 2 (13%) had non-nucleoside reverse transcriptase inhibitor (NNRTI) DRMs (K103N and Y181C) by bulk sequencing, whereas PGM detected 4 (26%) and MiSeq 5 (30%). NGS enabled the detection of additional minor variant DRMs in the infant with K103N. Coverage and instrument quality scores were higher with MiSeq, increasing the confidence of minor variant calls. CONCLUSIONS NGS followed by bioinformatic analyses detected multiple minor variant DRMs in HIV-1 RT among infants where PMTCT failed. The high coverage of MiSeq and high read quality improved the confidence of identified DRMs and may make this platform ideal for minor variant detection.
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The lysine 65 residue in HIV-1 reverse transcriptase function and in nucleoside analog drug resistance. Viruses 2014; 6:4080-94. [PMID: 25341667 PMCID: PMC4213578 DOI: 10.3390/v6104080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/19/2014] [Accepted: 10/20/2014] [Indexed: 12/04/2022] Open
Abstract
Mutations in HIV-1 reverse transcriptase (RT) that confer nucleoside analog RT inhibitor resistance have highlighted the functional importance of several active site residues (M184, Q151 and K65) in RT catalytic function. Of these, K65 residue is notable due to its pivotal position in the dNTP-binding pocket, its involvement in nucleoside analog resistance and polymerase fidelity. This review focuses on K65 residue and summarizes a substantial body of biochemical and structural studies of its role in RT function and the functional consequences of the K65R mutation.
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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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Singh K, Flores JA, Kirby KA, Neogi U, Sonnerborg A, Hachiya A, Das K, Arnold E, McArthur C, Parniak M, Sarafianos SG. Drug resistance in non-B subtype HIV-1: impact of HIV-1 reverse transcriptase inhibitors. Viruses 2014; 6:3535-62. [PMID: 25254383 PMCID: PMC4189038 DOI: 10.3390/v6093535] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus (HIV) causes approximately 2.5 million new infections every year, and nearly 1.6 million patients succumb to HIV each year. Several factors, including cross-species transmission and error-prone replication have resulted in extraordinary genetic diversity of HIV groups. One of these groups, known as group M (main) contains nine subtypes (A-D, F-H and J-K) and causes ~95% of all HIV infections. Most reported data on susceptibility and resistance to anti-HIV therapies are from subtype B HIV infections, which are prevalent in developed countries but account for only ~12% of all global HIV infections, whereas non-B subtype HIV infections that account for ~88% of all HIV infections are prevalent primarily in low and middle-income countries. Although the treatments for subtype B infections are generally effective against non-B subtype infections, there are differences in response to therapies. Here, we review how polymorphisms, transmission efficiency of drug-resistant strains, and differences in genetic barrier for drug resistance can differentially alter the response to reverse transcriptase-targeting therapies in various subtypes.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Jacqueline A Flores
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Karen A Kirby
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Anders Sonnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm 141 86, Sweden.
| | - Atsuko Hachiya
- Clinical Research Center, Department of Infectious Diseases and Immunology, National Hospital Organization, Nagoya Medical Center, Nagoya 460-0001, Japan.
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Carole McArthur
- Department of Oral and Craniofacial Science , School of Dentistry, University of Missouri, Kansas City, MO 64108, USA.
| | - Michael Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
| | - Stefan G Sarafianos
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
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Megens S, Laethem KV. HIV-1 genetic variation and drug resistance development. Expert Rev Anti Infect Ther 2014; 11:1159-78. [PMID: 24151833 DOI: 10.1586/14787210.2013.844649] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Up until 10 years ago, basic and clinical HIV-1 research was mainly performed on HIV-1 subtype B that predominated in resource-rich settings. Over the past decade, HIV-1 care and therapy has been scaled up substantially in Latin America, Africa and Asia. These regions are largely dominated by non-B subtype infections, and especially the African continent is affected by the HIV pandemic. Insight on the potency of antiviral drugs and regimens as well as on the emergence of drug resistance in non-B subtypes was lacking triggering research in this field, also partly driven by the introduction and spreading of HIV-1 non-B subtypes in Europe. The scope of this article was to review and discuss the state-of-the-art on the impact of HIV-1 genetic variation on the in vitro activity of antiviral drugs and in vivo response to antiviral therapy; as well as on the in vitro and in vivo emergence of drug resistance.
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Affiliation(s)
- Sarah Megens
- Department Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Grammatikos G, Jabara CB, Ahmad MQ, Herrmann E, Zeuzem S, Welsch C. Genetic background for development of resistance mutations within the HCV NS3 protease-helicase in direct acting antiviral naive patients. Antivir Ther 2013; 19:455-61. [PMID: 24457994 DOI: 10.3851/imp2734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Subtype-specific response to ketoamide NS3 protease inhibitors is observed in patients with genotype 1 HCV infection. Whether the genetic diversity in the molecular target site of ketoamide compounds prior to treatment plays a role for resistance development and lower treatment response in subtype 1a is poorly understood. METHODS Using a public database, we retrieved worldwide NS3-sequence information of 581 dominant HCV variants from patients chronically infected with genotype 1 that were naive to direct-acting antivirals. We applied measures from phylogeny to study the pretreatment genetic diversity and complexity in NS3 full-length as well as the protease-helicase interface for subtype 1a and 1b, respectively. RESULTS We found polymorphic sites more frequently in variants of subtype 1b than subtype 1a. Moreover, a significantly higher number of synonymous and non-synonymous substitutions were found in subtype 1b (P<0.001). Transitions were more frequent than transversions, most notably in subtype 1a, whereas the higher average number of nucleotide differences per site was found in subtype 1b. A comparison of NS3 full-length versus domain interface residues for both subtypes revealed a significant difference only for synonymous substitutions (P<0.001). CONCLUSIONS Our study suggests that the nature of a mismatch nucleotide exchange in NS3 may constitute an important viral genetic factor for response to ketoamide protease inhibitors. Our analysis further suggests that the subtype-specific pace of resistance development seen in clinical trials is not primarily related to differences in genetic diversity in the direct acting antiviral naive population, but rather appears to correlate with the natural frequency of transition mutations characteristic of each subtype.
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Affiliation(s)
- Georgios Grammatikos
- Department of Internal Medicine I, Frankfurt University Hospital, Goethe University, Frankfurt am Main, Germany
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Hosseinipour MC, Gupta RK, Van Zyl G, Eron JJ, Nachega JB. Emergence of HIV drug resistance during first- and second-line antiretroviral therapy in resource-limited settings. J Infect Dis 2013; 207 Suppl 2:S49-56. [PMID: 23687289 DOI: 10.1093/infdis/jit107] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
INTRODUCTION Antiretroviral therapy (ART) in resource-limited settings has expanded in the last decade, reaching >8 million individuals and reducing AIDS mortality and morbidity. Continued success of ART programs will require understanding the emergence of HIV drug resistance patterns among individuals in whom treatment has failed and managing ART from both an individual and public health perspective. We review data on the emergence of HIV drug resistance among individuals in whom first-line therapy has failed and clinical and resistance outcomes of those receiving second-line therapy in resource-limited settings. RESULTS Resistance surveys among patients initiating first-line nonnucleoside reverse-transcriptase inhibitor (NNRTI)-based therapy suggest that 76%-90% of living patients achieve HIV RNA suppression by 12 months after ART initiation. Among patients with detectable HIV RNA at 12 months, HIV drug resistance, primarily due to M184V and NNRTI mutations, has been identified in 60%-72%, although the antiretroviral activity of proposed second-line regimens has been preserved. Complex mutation patterns, including thymidine-analog mutations, K65R, and multinucleoside mutations, are prevalent among cases of treatment failure identified by clinical or immunologic methods. Approximately 22% of patients receiving second-line therapy do not achieve HIV RNA suppression by 6 months, with poor adherence, rather than HIV drug resistance, driving most failures. Major protease inhibitor resistance at the time of second-line failure ranges from 0% to 50%, but studies are limited. CONCLUSIONS Resistance of HIV to first-line therapy is predictable at 12 months when evaluated by means of HIV RNA monitoring and, when detected, largely preserves second-line therapy options. Optimizing adherence, performing resistance surveillance, and improving treatment monitoring are critical for long-term prevention of drug resistance.
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Santoro MM, Perno CF. HIV-1 Genetic Variability and Clinical Implications. ISRN MICROBIOLOGY 2013; 2013:481314. [PMID: 23844315 PMCID: PMC3703378 DOI: 10.1155/2013/481314] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
Despite advances in antiretroviral therapy that have revolutionized HIV disease management, effective control of the HIV infection pandemic remains elusive. Beyond the classic non-B endemic areas, HIV-1 non-B subtype infections are sharply increasing in previous subtype B homogeneous areas such as Europe and North America. As already known, several studies have shown that, among non-B subtypes, subtypes C and D were found to be more aggressive in terms of disease progression. Luckily, the response to antiretrovirals against HIV-1 seems to be similar among different subtypes, but these results are mainly based on small or poorly designed studies. On the other hand, differences in rates of acquisition of resistance among non-B subtypes are already being observed. This different propensity, beyond the type of treatment regimens used, as well as access to viral load testing in non-B endemic areas seems to be due to HIV-1 clade specific peculiarities. Indeed, some non-B subtypes are proved to be more prone to develop resistance compared to B subtype. This phenomenon can be related to the presence of subtype-specific polymorphisms, different codon usage, and/or subtype-specific RNA templates. This review aims to provide a complete picture of HIV-1 genetic diversity and its implications for HIV-1 disease spread, effectiveness of therapies, and drug resistance development.
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Affiliation(s)
- Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
- INMI L Spallanzani Hospital, Antiretroviral Therapy Monitoring Unit, Via Portuense 292, 00149 Rome, Italy
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Invernizzi CF, Coutsinos D, Oliveira M, Schildknecht RS, Xu H, Gaseitsiwe S, Moisi D, Brenner BG, Wainberg MA. The preferential selection of K65R in HIV-1 subtype C is attenuated by nucleotide polymorphisms at thymidine analogue mutation sites. J Antimicrob Chemother 2013; 68:2192-6. [PMID: 23749954 DOI: 10.1093/jac/dkt204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES We recently reported the preferential selection of the K65R resistance mutation in subtype C HIV-1 compared with subtype B and showed the underlying mechanism to be dependent on subtype C-specific silent nucleotide polymorphisms, i.e. genomic mutations that change the genotype but not the phenotype. The number of clinical reports demonstrating elevated numbers of K65R nevertheless suggests the existence of factors limiting the increased incidence of K65R mutations. Thus, we investigated the contributions of subtype C-specific silent nucleotide polymorphisms at thymidine analogue mutation (TAM) sites 70, 210 and/or 219 that might reduce the previously described preferential selection of K65R in subtype C HIV-1 associated with subtype C-specific nucleotide polymorphisms at sites 64/65. METHODS Cell culture drug selections were performed with various drugs in MT2 cells. RESULTS The use of nucleoside/nucleotide reverse transcriptase inhibitors [N(t)RTIs] as single drugs or in combination confirmed the more frequent selection of K65R by multiple N(t)RTIs in a subtype B virus that contained the 64/65 nucleotide polymorphisms of subtype C than in a wild-type subtype B virus. This effect was attenuated in the presence of several silent TAM nucleotide polymorphisms, except when stavudine was employed in the selection protocol. CONCLUSIONS These results further demonstrate that stavudine can preferentially select for K65R in subtype C virus and also provide a basis for understanding the importance of silent nucleotide polymorphisms in regard to altered HIV drug resistance profiles.
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Affiliation(s)
- Cédric F Invernizzi
- McGill University AIDS Centre, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, Montréal, Québec, Canada
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Identification and characterization of a novel HIV-1 nucleotide-competing reverse transcriptase inhibitor series. Antimicrob Agents Chemother 2013; 57:2712-8. [PMID: 23545531 DOI: 10.1128/aac.00113-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Several groups have recently reported on the identification of nucleotide-competing reverse transcriptase inhibitors (NcRTIs), a new class of RT inhibitors. NcRTIs reversibly inhibit binding of the incoming nucleotide to the RT active site but do not act as chain terminators, unlike the nucleos(t)ide reverse transcriptase inhibitor (NRTI) class. We identified a novel benzo[4,5]furo[3,2,d]pyrimidin-2-one NcRTI chemical series. Structure-activity relationship evaluation of this series with both RT and viral replication assays led to the identification of compound A, a new NcRTI. Compound A inhibited HIV-1 RT in a primer extension assay (50% inhibitory concentration, 2.6 nM) but had no measurable activity against human DNA polymerase γ at 10 μM. It potently inhibited HIV-1 replication in vitro (50% effective concentration, 1.5 nM). The antiviral potency of compound A was unaffected by the presence of nonnucleotide RT inhibitor (NNRTI) mutations tested (L100I, K103N/Y181C, V106A, or Y188L). Notably, viruses encoding K65R were hypersusceptible to inhibition by compound A. Compound A also retained full activity against viruses encoding M184V. In vitro selection for resistant virus to compound A led to the selection of a single substitution within RT: W153L. A recombinant virus encoding the RT W153L was highly resistant to compound A (fold change, 160). W153 is a highly conserved residue in HIV RT and has not been previously associated with drug resistance. In summary, a novel NcRTI series with optimized antiviral activity, minimal cross-resistance to existing RT inhibitor classes, and a distinct resistance profile has been discovered. These results further establish NcRTIs as an emerging class of antiretroviral agents.
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Menéndez-Arias L. Molecular basis of human immunodeficiency virus type 1 drug resistance: overview and recent developments. Antiviral Res 2013; 98:93-120. [PMID: 23403210 DOI: 10.1016/j.antiviral.2013.01.007] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/26/2013] [Accepted: 01/29/2013] [Indexed: 12/15/2022]
Abstract
The introduction of potent combination therapies in the mid-90s had a tremendous effect on AIDS mortality. However, drug resistance has been a major factor contributing to antiretroviral therapy failure. Currently, there are 26 drugs approved for treating human immunodeficiency virus (HIV) infections, although some of them are no longer prescribed. Most of the available antiretroviral drugs target HIV genome replication (i.e. reverse transcriptase inhibitors) and viral maturation (i.e. viral protease inhibitors). Other drugs in clinical use include a viral coreceptor antagonist (maraviroc), a fusion inhibitor (enfuvirtide) and two viral integrase inhibitors (raltegravir and elvitegravir). Elvitegravir and the nonnucleoside reverse transcriptase inhibitor rilpivirine have been the most recent additions to the antiretroviral drug armamentarium. An overview of the molecular mechanisms involved in antiretroviral drug resistance and the role of drug resistance-associated mutations was previously presented (Menéndez-Arias, L., 2010. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res. 85, 210-231). This article provides now an updated review that covers currently approved drugs, new experimental agents (e.g. neutralizing antibodies) and selected drugs in preclinical or early clinical development (e.g. experimental integrase inhibitors). Special attention is dedicated to recent research on resistance to reverse transcriptase and integrase inhibitors. In addition, recently discovered interactions between HIV and host proteins and novel strategies to block HIV assembly or viral entry emerge as promising alternatives for the development of effective antiretroviral treatments.
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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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26
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Bansode V, McCormack GP, Crampin AC, Ngwira B, Shrestha RK, French N, Glynn JR, Travers SA. Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing. BMC Infect Dis 2013; 13:52. [PMID: 23363532 PMCID: PMC3740783 DOI: 10.1186/1471-2334-13-52] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 01/28/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The role of HIV-1 RNA in the emergence of resistance to antiretroviral therapies (ARTs) is well documented while less is known about the role of historical viruses stored in the proviral DNA. The primary focus of this work was to characterize the genetic diversity and evolution of HIV drug resistant variants in an individual's provirus during antiretroviral therapy using next generation sequencing. METHODS Blood samples were collected prior to antiretroviral therapy exposure and during the course of treatment from five patients in whom drug resistance mutations had previously been identified using consensus sequencing. The spectrum of viral variants present in the provirus at each sampling time-point were characterized using 454 pyrosequencing from multiple combined PCR products. The prevalence of viral variants containing drug resistant mutations (DRMs) was characterized at each time-point. RESULTS Low abundance drug resistant viruses were identified in 14 of 15 sampling time-points from the five patients. In all individuals DRMs against current therapy were identified at one or more of the sampling time-points. In two of the five individuals studied these DRMs were present prior to treatment exposure and were present at high prevalence within the amplified and sequenced viral population. DRMs to drugs other than those being currently used were identified in four of the five individuals. CONCLUSION The presence of DRMs in the provirus, regardless of their observed prevalence did not appear to have an effect on clinical outcomes in the short term suggesting that the drug resistant viral variants present in the proviral DNA do not appear to play a role in the short term in facilitating the emergence of drug resistance.
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Affiliation(s)
- Vijay Bansode
- Molecular Evolution and Systematics laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Grace P McCormack
- Molecular Evolution and Systematics laboratory, Zoology, Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Amelia C Crampin
- Karonga Prevention Study, Chilumba, Malawi, South Africa
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Bagrey Ngwira
- Karonga Prevention Study, Chilumba, Malawi, South Africa
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Ram K Shrestha
- South African National Bioinformatics Institute, University of the Western, Cape, Bellville, South Africa
| | - Neil French
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Simon A Travers
- South African National Bioinformatics Institute, University of the Western, Cape, Bellville, South Africa
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Gonzalez S, Tully DC, Gondwe C, Wood C. Low-abundance resistant mutations in HIV-1 subtype C antiretroviral therapy-naive individuals as revealed by pyrosequencing. Curr HIV Res 2013; 11:43-49. [PMID: 23305169 PMCID: PMC4005869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 12/31/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
Given the recent scale-up of antiretroviral therapy (ART) in sub-Saharan Africa, we sought to determine how often and at what levels do drug-resistant mutant variants exist in ART-naive HIV subtype C infected individuals. Samples from 10 ART-naive Zambian individuals were subjected to ultra-deep pyrosequencing (UDPS) to characterize the frequency of low-abundance drug resistance mutations in the pol gene. Low-abundance clinically relevant variants were detected for nucleoside reverse transcriptase inhibitors (NRTIs), non-nucleoside reverse transcriptase inhibitors (NNRTIs) and protease inhibitors (PIs) in eight of the ten subjects. Intermediate to high-level resistance was predicted for the majority of NRTIs. Mutations conferring resistance to most first-line and some second-line therapy drugs were also observed. UDPS detected a number of additional major resistant mutations suggesting that these individuals may have an increased risk of virological failure after initiating ART. Moreover, the effectiveness of first-line and even some secondline ART may be compromised in this setting.
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Affiliation(s)
- Sandra Gonzalez
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
| | - Damien C. Tully
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
| | - Clement Gondwe
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
- Virology Department, University Teaching Hospital, P.O. Box 50223, Lusaka, 10101, Zambia
| | - Charles Wood
- Nebraska Center for Virology, Morrison Center, University of Nebraska-Lincoln, 4240 Fair St, Lincoln, NE 68583-0900, USA
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Götte M. The distinct contributions of fitness and genetic barrier to the development of antiviral drug resistance. Curr Opin Virol 2012; 2:644-50. [DOI: 10.1016/j.coviro.2012.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/15/2012] [Indexed: 01/14/2023]
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Lessells RJ, Katzenstein DK, de Oliveira T. Are subtype differences important in HIV drug resistance? Curr Opin Virol 2012; 2:636-43. [PMID: 23006584 DOI: 10.1016/j.coviro.2012.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 08/17/2012] [Accepted: 08/20/2012] [Indexed: 11/26/2022]
Abstract
The diversity of human immunodeficiency virus type 1 (HIV-1) has given rise to multiple subtypes and recombinant strains. The majority of research into antiretroviral agents and drug resistance has been performed on subtype B viruses, yet non-subtype B strains are responsible for 90% of global infections. Although it seems that combination antiretroviral regimens are effective against all HIV-1 subtypes, there is emerging evidence of subtype differences in drug resistance, relevant to antiretroviral strategies in different parts of the world. For this purpose, extensive sampling of HIV genetic diversity, curation and analyses are required to inform antiretroviral strategies in different parts of the world.
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Affiliation(s)
- R J Lessells
- Africa Centre for Health and Population Studies, University of KwaZulu-Natal, Somkhele, South Africa
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Recordon-Pinson P, Papuchon J, Reigadas S, Deshpande A, Fleury H. K65R in subtype C HIV-1 isolates from patients failing on a first-line regimen including d4T or AZT: comparison of Sanger and UDP sequencing data. PLoS One 2012; 7:e36549. [PMID: 22615779 PMCID: PMC3353948 DOI: 10.1371/journal.pone.0036549] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/09/2012] [Indexed: 12/03/2022] Open
Abstract
Background We and others have shown that subtype C HIV-1 isolates from patients failing on a regimen containing stavudine (d4T) or zidovudine (AZT) exhibit thymidine-associated mutations (TAMs) and K65R which can impair the efficacy of Tenofovir (TDF) at second line. Depending on the various studies, the prevalence of K65R substitution as determined by the Sanger method ranges from 4 to 30%. Our aim was to determine whether ultra-deep pyrosequencing (UDPS) could provide more information than the Sanger method about selection of K65R in this population of patients. Methods 27 subtype C HIV-1 isolates from treated patients failing on a regimen with d4T or AZT plus lamivudine (3TC) plus nevirapine (NVP) or efavirenz (EFV) and who had been sequenced by Sanger were investigated by UDPS at codon 65 of the reverse transcriptase (RT). 18 isolates from naïve patients and dilutions of a control K65R plasmid were analysed by Sanger plus UDPS. Results Analysis of Sanger sequences of subtype C HIV-1 isolates from naïve patients exhibited expected polymorphic substitutions compared to subtype B but no drug resistance mutations (DRMs). Quantitation of K65R variants by UDPS ranged from <0.4% to 3.08%. Sanger sequences of viral isolates from patients at failure of d4T or AZT plus 3TC plus NVP or EFV showed numerous DRMs to nucleoside reverse transcriptase inhibitors (NRTIs) including M184V, thymidine-associated mutations (TAMs) plus DRMs to non- nucleoside reverse transcriptase inhibitors (NNRTIs). Two K65R were observed by Sanger in this series of 27 samples with UDPS percentages of 27 and 87%. Other samples without K65R by Sanger exhibited quantities of K65R variants ranging from <0.4% to 0.80%, which were below the values observed in isolates from naïve patients. Conclusions While Sanger sequencing of subtype C isolates from treated patients at failure of d4T or AZT plus 3TC plus NVP or EFV exhibited numerous mutations including TAMs and 8% K65R, UDPS quantitation of K65R variants in the same series did not provide any more information than Sanger.
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Affiliation(s)
- Patricia Recordon-Pinson
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | - Jennifer Papuchon
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | - Sandrine Reigadas
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
| | | | - Hervé Fleury
- CNRS, UMR 5234, Bordeaux, France
- Laboratoire de Virologie (WHO accredited), CHU de Bordeaux, Bordeaux, France
- * E-mail:
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Hamers RL, Sigaloff KCE, Wensing AM, Wallis CL, Kityo C, Siwale M, Mandaliya K, Ive P, Botes ME, Wellington M, Osibogun A, Stevens WS, Rinke de Wit TF, Schuurman R. Patterns of HIV-1 drug resistance after first-line antiretroviral therapy (ART) failure in 6 sub-Saharan African countries: implications for second-line ART strategies. Clin Infect Dis 2012; 54:1660-9. [PMID: 22474222 DOI: 10.1093/cid/cis254] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus type 1 (HIV-1) drug resistance may limit the benefits of antiretroviral therapy (ART). This cohort study examined patterns of drug-resistance mutations (DRMs) in individuals with virological failure on first-line ART at 13 clinical sites in 6 African countries and predicted their impact on second-line drug susceptibility. METHODS A total of 2588 antiretroviral-naive individuals initiated ART consisting of different nucleoside reverse transcriptase inhibitor (NRTI) backbones (zidovudine, stavudine, tenofovir, or abacavir, plus lamivudine or emtricitabine) with either efavirenz or nevirapine. Population sequencing after 12 months of ART was retrospectively performed if HIV RNA was >1000 copies/mL. The 2010 International Antiviral Society-USA list was used to score major DRMs. The Stanford algorithm was used to predict drug susceptibility. RESULTS HIV-1 sequences were generated for 142 participants who virologically failed ART, of whom 70% carried ≥1 DRM and 49% had dual-class resistance, with an average of 2.4 DRMs per sequence (range, 1-8). The most common DRMs were M184V (53.5%), K103N (28.9%), Y181C (15.5%), and G190A (14.1%). Thymidine analogue mutations were present in 8.5%. K65R was frequently selected by stavudine (15.0%) or tenofovir (27.7%). Among participants with ≥1 DRM, HIV-1 susceptibility was reduced in 93% for efavirenz/nevirapine, in 81% for lamivudine/emtricitabine, in 59% for etravirine/rilpivirine, in 27% for tenofovir, in 18% for stavudine, and in 10% for zidovudine. CONCLUSIONS Early failure detection limited the accumulation of resistance. After stavudine failure in African populations, zidovudine rather than tenofovir may be preferred in second-line ART. Strategies to prevent HIV-1 resistance are a global priority.
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Affiliation(s)
- Raph L Hamers
- PharmAccess Foundation, Academic Medical Center of the University of Amsterdam, The Netherlands.
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Kozal MJ, Chiarella J, St John EP, Moreno EA, Simen BB, Arnold TE, Lataillade M. Prevalence of low-level HIV-1 variants with reverse transcriptase mutation K65R and the effect of antiretroviral drug exposure on variant levels. Antivir Ther 2012; 16:925-9. [PMID: 21900725 DOI: 10.3851/imp1851] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
BACKGROUND It has been reported that treatment-naive individuals infected with HIV-1 subtype C may be more likely to harbour viral variants possessing a K65R reverse transcriptase gene mutation. The objectives of this study were to determine the prevalence of low-level K65R variants within different HIV-1 subtypes and to assess the effects of antiretroviral exposure on K65R variant levels. METHODS Treatment-naive individuals infected with different HIV-1 subtypes were genotyped by ultra-deep sequencing. Samples were evaluated for low-level variants to 0.4% or 1% levels depending upon viral load. Estimated mutational load was calculated by multiplying the percentage of the variant by the plasma viral load. RESULTS A total of 411 treatment-naive individuals were evaluated by ultra-deep sequencing to 1% levels; 4 subjects (0.97%) had K65R variants at ≥1% or had a very high mutation load. All four subjects had variants with linked drug resistance mutations suggesting transmitted resistant variants. 147 ARV-naive subjects were sequenced to 0.4% levels; 8.8% (13/147) had K65R low-level variants identified: 2.2% (2/92) in subtype B, 35.7% (10/28) in subtype C (P<0.001 for B versus C) and 3.7% (1/27) in non-B/C subtypes. The 13 ARV-naive subjects with K65R variants at <1% received tenofovir plus emtricitabine plus a ritonavir-boosted protease inhibitor (TDF+FTC+PI/r) and 5 subsequently experienced virological failure. There was no enhancement in K65R levels by percentage or mutational load compared to pre-therapy levels. CONCLUSIONS Low-level K65R variants were more frequently identified in subtype C. K65R variants at >1% levels likely represent transmitted resistant variants. The clinical implication of low-level K65R variants below 1% in treatment-naive subjects who receive TDF+FTC+PI/r remains to be determined as the majority are very low-level and did not increase after antiretroviral exposure.
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Affiliation(s)
- Michael J Kozal
- Yale University School of Medicine and Veterans Affairs Connecticut Healthcare System, New Haven, CT, USA.
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Bertagnolio S, De Luca A, Vitoria M, Essajee S, Penazzato M, Hong SY, McClure C, Duncombe C, Jordan MR. Determinants of HIV drug resistance and public health implications in low- and middle-income countries. Antivir Ther 2012; 17:941-53. [DOI: 10.3851/imp2320] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2012] [Indexed: 10/28/2022]
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